USPTO Patents Application 09847113

PATENT
A69306-1/RFT/RMS/RMK

5

10

TARGET ANALYTE DETECTION USING ASYMMETRICAL SELF-ASSEMBLED MONOLAYERS

i-B

11 This application claims the benefit of U.S. S.N. 60/201,026, filed May 1, 2000 and is a continuation in

M part application of U. S.S.N. 09/626,096, filed July 26, 2000.

B 20 FIELD OF THE INVENTION

H The present invention relates to the use asymmetric monolayer forming species and electroconduit

? * forming species to detect target analytes.

25 BACKGROUND OF THE INVENTION

There are a number of assays and sensors for the detection of the presence and/or concentration of
specific substances in fluids and gases. Many of these rely on specific ligand/antiligand reactions as
the mechanism of detection. That is, pairs of substances (i.e. the binding pairs or ligand/antiligands)
30 are known to bind to each other, while binding little or not at all to other substances. This has been

the focus of a number of techniques that utilize these binding pairs for the detection of the complexes.
These generally are done by labeling one component of the complex in some way, so as to make the
entire complex detectable, using, for example, radioisotopes, fluorescent and other optically active
molecules, enzymes, etc.

35

Other assays rely on electronic signals for detection. Of particular interest are biosensors. At least
two types of biosensors are known; enzyme-based or metabolic biosensors and binding or bioaffinity

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sensors. See for example U.S. Patent No. 4,713,347; 5,192,507; 4,920,047; 3,873,267; and
references disclosed therein. While some of these known sensors use alternating current (AC)
techniques, these techniques are generally limited to the detection of differences in bulk (or dielectric)
impedance.

5

The use of self-assembled monolayers (SAMs) on surfaces for binding and detection of biological
molecules has recently been explored. See for example WO98/20162; PCT US98/12430; PCT
US98/12082; PCT US99/01705; PCT/US99/21683; PCT/US99/10104; PCT/US99/01703;
PCT/US00/31233; U.S. Patent Nos. 5,620,850; 6,197,515; 6,013,459; 6,013,170; and 6,065,573; and
1 0 references cited therein.

Accordingly, it is an object of the invention to provide novel methods and compositions for the
electronic detection of target analytes using self-assembled monolayers.

15 SUMMARY OF THE INVENTION

In accordance with the objects outlined above, the present invention provides compositions comprising
metallic surfaces comprising asymmetric monolayer forming species comprising two components.
One of the components is a standard monolayer forming species, such an alkyl chain. The other
20 component is an electroconduit forming species. Electroconduit forming species are short chain alkyl
groups, which may be branched.

In a further embodiment, the invention provides methods of detecting a target analyte in a test sample
comprising attaching said target analyte to a metallic surface comprising asymmetric monolayer
25 forming species via binding to a capture binding ligand. Recruitment linkers, or label probes are
directly or indirectly attached to the target analyte to form an assay complex. The method further
comprises detecting electron transfer between an electron transfer moiety and an electrode.

BRIEF DESCRIPTION OF THE DRAWINGS

30

Figures 1A-1 R depict a number of different compositions of the invention. Figure 1 A depicts I, also
referred to as P290. Figure 1 B depicts II, also referred to as P291 . Figure 1 C depicts III, also referred
to as W31. Figure 1 D depicts IV, also referred to as N6. Figure 1E depicts V, also referred to as
P292. Figure 1F depicts II, also referred to as C23. Figure 1G depicts VII, also referred to as C15.
35 Figure 1H depicts VIII, also referred to as C95. Figure 11 depicts Y63. Figure 1J depicts another

compound of the invention. Figure 1K depicts N11. Figure 1L depicts C1 31, with a phosphoramidite
group and a DMT protecting group. Figure 1 M depicts W38, also with a phosphoramidite group and a

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DMT protecting group. Figure 1N depicts the commercially available moiety that enables "branching"
to occur, as its incorporation into a growing oligonucleotide chain results in addition at both the DMT
protected oxygens. Figure 10 depicts glen, also with a phosphoramidite group and a DMT protecting
group, that serves as a non-nucleic acid linker. Figures 1A to 1G and 1J are shown without the
5 phosphoramidite and protecting groups (i.e. DMT) that are readily added.

Figures 2A, 2B and 2C depict some useful disulfide embodiments. Figure 2A depicts one example of
a general class of an asymmetric monolayer forming species. Figure 2B depicts two embodiments that
were used to generate the data shown in Figure 2C. In Figure 2C, M44 is a standard monolayer
10 forming species; the structure of M44 is shown in Figure

Figures 3A, 3B, 3C, 3D, 3E, 3F and 3G depict the synthesis of some disulfide embodiments. Figure
3A depicts the general synthesis; with R, R' and R" being C1 to C20 alkyl or aromatic derivatives and
B being any base such as HaOH, KOH, LiOH or MOR, with M being a metal. Figure 3B shows the
1 5 synthesis of H-phosphonate, Figures 3C and 3D show the synthesis of the CPG derivative, and Figure
3E shows the synthesis of the insulator CT1 05. 3F and 3G depict some cyclic disulfide embodiments.

Figures 4A, 4B and 4C depict three preferred embodiments for attaching a target nucleic acid
sequence to the electrode. Figure 4A depicts a target sequence 120 hybridized to a capture probe 100

20 linked via a attachment linker 106, which as outlined herein may be either a conductive oligomer or an
insulator. The electrode 105 comprises a monolayer 107 comprising asymmetric monolayer forming
species, i.e., alkyl chains 400 and electroconduit forming species 410 (which may be short branched
alkyl chains, short alkyl chains, or a mixture of branched and short alkyl chains). As for all the
embodiments depicted in the figures, n is an integer of at least 1, although as will be appreciated by

25 those in the art, the system may not utilize a capture probe at all (i.e. n is zero), although this is

generally not preferred. The upper limit of n will depend on the length of the target sequence and the
required sensitivity. Figure 4B depicts the use of a single capture extender probe 110 with a first
portion 111 that will hybridize to a first portion of the target sequence 120 and a second portion that
will hybridize to the capture probe 100. Figure 4C depicts the use of two capture extender probes 110

30 and 130. The first capture extender probe 110 has a first portion 111 that will hybridize to a first

portion of the target sequence 120 and a second portion 112 that will hybridize to a first portion 102 of
the capture probe 100. The second capture extender probe 130 has a first portion 132 that will
hybridize to a second portion of the target sequence 120 and a second portion 131 that will hybridize
to a second portion 101 of the capture probe 100. As will be appreciated by those in the art, while

35 these systems depict nucleic acid targets, these attachment configurations may be used with non-
nucleic acid capture binding ligands.

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Figure 5A, 5B, 5C and 5D depict several embodiments of the invention. Figure 5A is directed to the
use of a capture binding ligand 200 attached via an attachment linker 106 to the electrode 105. Target
analyte 210 binds to the capture binding ligand 200, and a solution binding ligand 22 with a directly
attached recruitment linker 230 with ETMs 135. Figure 5B depicts a similar embodiment using an
5 indirectly attached recruitment linker 145 that binds to a second portion 240 of the solution binding

ligand 220. Figure 5C depicts the use of an anchor ligand 100 (referred to herein as an anchor probe
when the ligand comprises nucleic acid) to bind the capture binding ligand 200 comprising a portion
120 that will bind to the anchor probe 100. As will be appreciated by those in the art, any of the Figure
4 embodiments may be used here as well. Figure 5D depicts the use of an amplifier probe 145.

10

Figures 6A and 6B show two competitive type assays of the invention. Figure 6A utilizes the
replacement of a target analyte 210 with a target analyte analog 310 comprising a directly attached
recruitment linker 145. As will be appreciated by those in the art, an indirectly attached recruitment
linker can also be used, as shown in Figure 6B. Figure 6B shows a competitive assay wherein the
15 target analyte 210 and the target analyte analog 310 attached to the surface compete for binding of a v
solution binding ligand 220 with a directly attached recruitment linker 145 (again, an indirectly attached
recruitment linker can also be used, as shown in Figure 5B). In this case, a loss of signal may be
seen.

20 Figures 7A-7R depict nucleic acid detection systems. Figures 7A and 7B have the target sequence 5
containing the ETMs 6; as discussed herein, these may be added enzymatically, for example during a
PCR reaction using nucleotides modified with ETMs, resulting in essentially random incorporation
throughout the target sequence, or added to the terminus of the target sequence. Figure 7A shows
attachment of a capture probe 10 to the electrode 20 via a linker 15, which as discussed herein can be

25 either a conductive oligomer or an insulator. The target sequence 5 contains ETMs 6. Figure 7B
depicts the use of a capture extender probe 11, comprising a first portion 12 that hybridizes to a
portion of the target sequence and a second portion 13 that hybridizes to the capture probe 10.

Figure 7C depicts the use of two different capture probes 10 and 10', that hybridize to different
30 portions of the target sequence 5. As will be appreciated by those in the art, the 5'-3' orientation of the
two capture probes in this embodiment is different.

Figures 7D to 7H depict the use of label probes 40 that hybridize directly to the target sequence 5.
Figure 7D shows the use of a label probe 40, comprising a first portion 41 that hybridizes to a portion
35 of the target sequence 5, a second portion 42 that hybridizes to the capture probe 10 and a

recruitment linker 50 comprising ETMs 6. A similar embodiment is shown in Figure 7E, where the
label probe 40 has an additional recruitment linker 50. Figure 7F depicts a label probe 40 comprising

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a first portion 41 that hybridizes to a portion of the target sequence 5 and a recruitment linker 50 with
attached ETMs 6. The parentheses highlight that for any particular target sequence 5 more than one
label probe 40 may be used, with n being an integer of at least 1 . Figure 7G depicts the use of the
Figure 7E label probe structures but includes the use of a single capture extender probe 11, with a first

5 portion 12 that hybridizes to a portion of the target sequence and a second portion 13 that hybridizes
to the capture probe 10. Figure 7H depicts the use of the Figure 7F label probe structures but utilizes
two capture extender probes 11 and 16. The first capture extender probe 11 has a first portion 12 that
hybridizes to a portion of the target sequence 5 and a second portion 13 that hybridizes to a first
portion 14 of the capture probe 10. The second capture extender probe 16 has a first portion 18 that

1 0 hybridizes to a second portion of the target sequence 5 and a second portion 17 that hybridizes to a
second portion 19 of the capture probe 10.

Figures 71, 7J and 7K depict systems utilizing label probes 40 that do not hybridize directly to the
target, but rather to amplifier probes. Thus the amplifier probe 60 has a first portion 65 that hybridizes
15 to the target sequence 5 and at least one second portion 70, i.e. the amplifier sequence, that
hybridizes to the first portion 41 of the label probe.

Figures 7L, 7M and 7N depict systems that utilize a first label extender probe 80. In these
embodiments, the label extender probe 80 has a first portion 81 that hybridizes to a portion of the
20 target sequence 5, and a second portion 82 that hybridizes to the first portion 65 of the amplifier probe
60.

Figure 70 depicts the use of two label extender probes 80 and 90. The first label extender probe 80
has a first portion 81 that hybridizes to a portion of the target sequence 5, and a second portion 82 that
25 hybridizes to a first portion 62 of the amplifier probe 60. The second label extender probe 90 has a
first portion 91 that hybridizes to a second portion of the target sequence 5 and a second portion 92
that hybridizes to a second portion 61 of the amplifier probe 60.

Figure 7P depicts a system utilizing a label probe 40 hybridizing to the terminus of a target sequence
30 5.

Figures 7Q and 7R depict systems that utilizes multiple label probes. The first portion 41 of the label
probe 40 can hybridize to all (Figure 7R) or part (Figure 7Q) of the recruitment linker 50.

35 Figure 8 depicts a detection system with a label probe labeled with multiple ETMs, in which a first

portion hybridizes to a portion of a target sequence and a capture probe that hybridizes to a different
portion of the target sequence.

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Figure 9 depicts the chemical structures of a standard monolayer forming species, M44 and two
asymmetrical monolayer forming species, CT99 and CT105.

Figure 10 depicts an example of a layout for an array chip with sensor pads.

5

Figure 11 depicts the electrochemical response of asymmetric monolayer forming species vs a
standard monolayer forming species in a direct assay using a 2 N6 ferrocene signaling probe.

Figure 12 depicts the electrochemical response of asymmetric monolayer forming species vs a
1 0 standard monolayer forming species a sandwich assay using 8 N6 ferrocene.

Figure 13 depicts the electrochemical response of asymmetric monolayer forming species versus a
standard monolayer forming species a sandwich assay using a 20 C23 type ferrocene.

15 Figure 14 depicts the electrochemical response of asymmetric monolayer forming species vs a
standard monolayer forming species a sandwich assay using a 54 C23 type ferrocene.

Figure 15 depicts the nonspecific binding of asymmetric monolayer forming species versus a standard
monolayer forming species in a direct assay at 1000 Hz and 4 th harmonics.

20

Figure 16 depicts the nonspecific binding of asymmetric monolayer forming species versus a standard
monolayer forming species in a sandwich assay at 1000 Hz and 4 th harmonics.

Figure 17 depicts a monolayer comprising insulators only (i.e. M44) and a monolayer comprising
25 asymmetric monolayer forming species (i.e. CT105).

Figure 18 depicts the frequency response for D1085 of two N6 ferrocenes.

Figure 19 depicts the frequency response for a sandwich assay of an 8 ferrocene system.

30

Figure 20 depicts the frequency response for a sandwich assay of an 20 ferrocene system.

DETAILED DESCRIPTION OF THE INVENTION

35 The present invention is directed to the electronic detection of analytes. Previous work, described in
PCT US97/20014, is directed to the detection of nucleic acids, and utilizes nucleic acids covalently
attached to electrodes using conductive oligomers, i.e. chemical "wires". Upon formation of double

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stranded nucleic acids containing electron transfer moieties (ETMs), electron transfer can proceed
through the stacked n-orbitals of the heterocyclic bases to the electrode, thus enabling electronic
detection of target nucleic acids (termed "mechanism 1"). In the absence of the stacked n-orbitals, i.e.
when the target strand is not present, electron transfer is negligible, thus allowing the use of the
5 system as an assay. This previous work also reported on the use of self-assembled monolayers

(SAMs) to electronically shield the electrodes from solution components and significantly decrease the
amount of non-specific binding to the electrodes.

Alternatively, the ETM can be detected, not necessarily via electron transfer through nucleic acid, but

10 rather can be directly detected on an electrode comprising a SAM; that is, the electrons from the ETMs
need not travel through the stacked n orbitals in order to generate a signal. As above, in this
embodiment, the detection electrode preferably comprises a self-assembled monolayer (SAM) that
serves to shield the electrode from redox-active species in the sample. In this embodiment, the
presence of ETMs on the surface of a SAM, that has been formulated to comprise slight "defects"

15 (sometimes referred to herein as "microconduits", "nanoconduits" or "electroconduits") can be directly
detected. This basic idea is termed "mechanism-2" herein. Essentially, the electroconduits allow
particular ETMs access to the surface. Upon binding of a target analyte to a binding species on the
surface, a recruitment linker or label probe comprising at least one ETM is brought to the surface, and
detection of the ETM can proceed. Thus, the role of the target analyte and binding species is to

20 provide specificity for a recruitment of ETMs to the surface, where they can be detected using the

electrode. The role of the asymmetric monolayer species comprising the defects is to allow contact of
the ETM with the electronic surface of the electrode, while still providing the benefits of shielding the
electrode from solution components and reducing the amount of non-specific binding to the electrodes.
See, for example, WO98/20162; PCT US98/12430; PCT US98/12082; PCT US99/01705;

25 PCT/US99/21683; PCT/US99/10104; PCT/US99/01703; PCT/USOO/20476; PCT/US00/31233; U.S.

Patent Nos. 5,620,850; 6,197,515; 6,013,459; 6,013,170; and 6,065,573; and U.S.S.N.s 09/660,374;
and, 09/135,183 and references cited therein.

Thus, the present invention is directed to novel compositions of monolayer forming species that are
30 thought to form electroconduits; that is, the present invention is directed to the use of monolayers

comprising asymmetric monolayer forming species ("AMFS"). As described more fully below, AMFS
comprise two components, usually linked by a disulfide bridge, at least one of which is a standard
monolayer forming species such as an alkyl chain, and the other is a shorter species, for example a
shorter alkyl chain or a short branched chain. These two elements are put down together, for example
35 by attaching them as a disulfide moiety that then is used to form a monolayer on a metallic surface

such as gold. The "shorter" element thus, is thought to form an electroconduit, and protect the surface
from redox-active species in solution.

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A

Without being bound by theory, it should be noted that the configuration of the electroconduit depends
in part on the ETM chosen. For example, the use of relatively hydrophobic ETMs allows the use of
hydrophobic electroconduit forming species, which effectively exclude hydrophilic or charged ETMs.
Similarly, the use of more hydrophilic or charged species in the SAM may serve to exclude
5 hydrophobic ETMs.

Asymmetric monolayer forming species preferably comprise a mixture of insulators and electroconduit
forming species, although conductive oligomers as either component, also may be included.
Preferably, the insulators are long chain alkyl groups from about 7 to 20 carbons in length which are
10 covalently attached to a metallic surface via a linker moiety such as sulfur. Electroconduit forming
species include alkyl groups, phenyl-acetylene-polyethylene glycol species, and branched alkyl
groups. In addition asymmetric monolayer forming species include asymmetrical SAM-forming
disulfide species such as depicted in Figure 3.

15 The invention can be generally described as follows, with a number of possible embodiments depicted
in the Figures. In a preferred embodiment, as depicted in Figure 5, an electrode comprising an
asymmetric monolayer forming species comprising insulators (preferably a long chain alkyl group), an
electroconduit forming species, and a covalently attached target anaiyte binding ligand (frequently
referred to herein as a "capture binding ligand") is made. The target anaiyte is added, which binds to

20 the support-bound binding ligand. A solution binding ligand is added, which may be the same or

different from the first binding ligand, which can also bind to the target anaiyte, forming a "sandwich" of
sorts. The solution binding ligand either comprises a recruitment linker containing ETMs, or comprises
a portion that will either directly or indirectly bind a recruitment linker containing the ETMs. This
"recruitment" of ETMs to the surface of the monolayer allows electronic detection via electron transfer

25 between the ETM and the electrode. In the absence of the target anaiyte, the recruitment linker is
either washed away or not in sufficient proximity to the surface to allow detection.

For example, when both the target anaiyte and the capture binding ligand (generally referred to herein
as a "capture probe" when it is a nucleic acid) are nucleic acids, a preferred embodiment is shown in
30 Figure 8. In this embodiment, the surface comprises an AMFS and a capture probe. A first portion of
the target sequence hybridizes to the capture probe, and a label probe, comprising a recruitment linker
comprising ETMs, hybridizes to a second portion of the target sequence.

In an alternate preferred embodiment, as depicted in Figure 6, a competitive binding type assay is run.
35 In this embodiment, the target anaiyte in the sample is replaced by a target anaiyte analog as is

described below and generally known in the art. The analog comprises a directly or indirectly attached
recruitment linker comprising at least one ETM. The binding of the analog to the capture binding

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tigand recruits the ETM to the surface and allows detection based on electron transfer between the
ETM and the electrode.

In an additional preferred embodiment, as depicted in Figure 6B, a competitive assay wherein the
5 target analyte and a target analyte analog attached to the surface compete for binding of a solution

binding ligand with a directly or indirectly attached recruitment linker. In this case, a loss of signal may
be seen.

Accordingly, the present invention provides methods and compositions useful in the detection of target
10 analytes. As will be appreciated by those in the art, the sample solution may comprise any number of
things, including, but not limited to, bodily fluids (including, but not limited to, blood, urine, serum,
lymph, saliva, anal and vaginal secretions, perspiration and semen, of virtually any organism, with
mammalian samples being preferred and human samples being particularly preferred); environmental
samples (including, but not limited to, air, agricultural, water and soil samples); biological warfare
15 agent samples; research samples (i.e. in the case of nucleic acids, the sample may be the products of
an amplification reaction, including both target and signal amplification as is generally described in
PCT/US99/01705, such as PCR amplification reaction); purified samples, such as purified genomic
DNA, RNA, proteins, etc.; raw samples (bacteria, virus, genomic DNA, etc.). As will be appreciated by
those in the art, virtually any experimental manipulation may have been done on the sample.

20

By "target analyte" or "analyte" or grammatical equivalents herein is meant any molecule or compound
to be detected and that can bind to a binding species, defined below. Suitable analytes include, but
not limited to, small chemical molecules such as environmental or clinical chemical or pollutant or
biomolecule, including, but not limited to, pesticides, insecticides, toxins, therapeutic and abused

25 drugs, hormones, antibiotics, antibodies, organic materials, etc. Suitable biomolecules include, but are
not limited to, proteins (including enzymes, immunoglobulins and glycoproteins), nucleic acids, lipids,
lectins, carbohydrates, hormones, whole cells (including procaryotic (such as pathogenic bacteria) and
eucaryotic cells, including mammalian tumor cells), viruses, spores, etc. Particularly preferred
analytes are proteins including enzymes; drugs, cells; antibodies; antigens; cellular membrane

30 antigens and receptors (neural, hormonal, nutrient, and cell surface receptors) or their ligands.

By "proteins" or grammatical equivalents herein is meant proteins, oligopeptides and peptides, and
analogs, including proteins containing non-naturally occurring amino acids and amino acid analogs,
and peptidomimetic structures.

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As will be appreciated by those in the art, a large number of analytes may be detected using the
present methods; basically, any target analyte for which a binding ligand, described below, may be
made may be detected using the methods of the invention.

5 By "nucleic acid" or "oligonucleotide" or grammatical equivalents herein means at least two

nucleotides covalently linked together. A nucleic acid of the present invention will generally contain
phosphodiester bonds, although in some cases, as outlined below, nucleic acid analogs are included
that may have alternate backbones, comprising, for example, phosphoramide (Beaucage et al.,
Tetrahedron 49(10):1925 (1993) and references therein; Letsinger, J. Org. Chem. 35:3800 (1970);

10 Sprinzl etal., Eur. J. Biochem. 81:579 (1977); Letsinger et al., Nucl. Acids Res. 14:3487 (1986); Sawai
et al, Chem. Lett. 805 (1984), Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988); and Pauwels etal.,
Chemica Scripta 26:141 91986)), phosphorothioate (Mag et al., Nucleic Acids Res. 19:1437 (1991);
and U.S. Patent No. 5,644,048), phosphorodithioate (Briu etal., J. Am. Chem. Soc. 111:2321 (1989),
O-methylphophoroamidite linkages (see Eckstein, Oligonucleotides and Analogues: A Practical

15 Approach, Oxford University Press), and peptide nucleic acid backbones and linkages (see Egholm, J.
Am. Chem. Soc. 114:1895 (1992); Meier et al., Chem. Int. Ed. Engl. 31:1008 (1992); Nielsen, Nature,
365:566 (1993); Carlsson et al., Nature 380:207 (1996), all of which are incorporated by reference).
Other analog nucleic acids include those with positive backbones (Denpcy et al., Proc. Natl. Acad. Sci.
USA 92:6097 (1995); those with bicyclic structures including locked nucleic acids, Koshkin et al., J.

20 Am. Chem. Soc. 120:13252-3 (1998); non-ionic backbones (U.S. Patent Nos. 5,386,023, 5,637,684,
5,602,240, 5,216,141 and 4,469,863; Kiedrowshi etal., Angew. Chem. Intl. Ed. English 30:423 (1991);
Letsinger etal., J. Am. Chem. Soc. 110:4470 (1988); Letsinger et al., Nucleoside & Nucleotide
13:1597 (1994); Chapters 2 and 3, ASC Symposium Series 580, "Carbohydrate Modifications in
Antisense Research", Ed. Y.S. Sanghui and P. Dan Cook; Mesmaeker et al., Bioorganic & Medicinal

25 Chem. Lett. 4:395 (1994); Jeffs et al., J. Biomolecular NMR 34:17 (1994); Tetrahedron Lett. 37:743
(1996)) and non-ribose backbones, including those described in U.S. Patent Nos. 5,235,033 and
5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, "Carbohydrate Modifications in
Antisense Research", Ed. Y.S. Sanghui and P. Dan Cook. Nucleic acids containing one or more
carbocyclic sugars are also included within the definition of nucleic acids (see Jenkins et al., Chem.

30 Soc. Rev. (1995) pp169-176). Several nucleic acid analogs are described in Rawls, C & E News

June 2, 1997 page 35. All of these references are hereby expressly incorporated by reference. These
modifications of the ribose-phosphate backbone may be done to facilitate the addition of ETMs, or to
increase the stability and half-life of such molecules in physiological environments.

35 As will be appreciated by those in the art, all of these nucleic acid analogs may find use in the present
invention. In addition, mixtures of naturally occurring nucleic acids and analogs can be made.

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Alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic
acids and analogs may be made.

Particularly preferred are peptide nucleic acids (PNA) which includes peptide nucleic acid analogs.

5 These backbones are substantially non-ionic under neutral conditions, in contrast to the highly
charged phosphodiester backbone of naturally occurring nucleic acids. This results in two
advantages. First, the PNA backbone exhibits improved hybridization kinetics. PNAs have larger
changes in the melting temperature (Tm) for mismatched versus perfectly matched basepairs. DNA
and RNA typically exhibit a 2-4°C drop in Tm for an internal mismatch. With the non-ionic PNA

10 backbone, the drop is closer to 7-9°C. Similarly, due to their non-ionic nature, hybridization of the
bases attached to these backbones is relatively insensitive to salt concentration. This is particularly
advantageous in the systems of the present invention, as a reduced salt hybridization solution has a
lower Faradaic current than a physiological salt solution (in the range of 150 mM).

15 The nucleic acids may be single stranded or double stranded, as specified, or contain portions of both
double stranded or single stranded sequence. The nucleic acid may be DNA, both genomic and
cDNA, RNA or a hybrid, where the nucleic acid contains any combination of deoxyribo- and ribo-
nucleotides, and any combination of bases, including uracil, adenine, thymine, cytosine, guanine,
inosine, xathanine hypoxathanine, isocytosine, isoguanine, etc. A preferred embodiment utilizes

20 isocytosine and isoguanine in nucleic acids designed to be complementary to other probes, rather
than target sequences, as this reduces non-specific hybridization, as is generally described in U.S.
Patent No. 5,681,702. As used herein, the term "nucleoside" includes nucleotides as well as
nucleoside and nucleotide analogs, and modified nucleosides such as amino modified nucleosides. In
addition, "nucleoside" includes non-naturally occuring analog structures. Thus for example the

25 individual units of a peptide nucleic acid, each containing a base, are referred to herein as a
nucleoside.

As will be appreciated by those in the art, a large number of analytes may be detected using the
present methods; basically, any target analyte for which a binding ligand, described below, may be
30 made may be detected using the methods of the invention.

Accordingly, the present invention provides methods and compositions useful in the detection of target
analytes. In a preferred embodiment, the compositions comprise a substrate comprising a metallic
surface comprising an asymmetric monolayer forming species.

35

By "substrate" or "solid support" or other grammatical equivalents herein is meant any material that
can be modified to contain discrete individual sites appropriate for the attachment or association of

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target analytes. The substrate can comprise a wide variety of materials, as will be appreciated by
those in the art, with printed circuit board (PCB) materials being particularly preferred. Other suitable
substrates include, but are not limited to, metal surfaces such as gold, electrodes as defined below,
glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of
5 styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes), Teflon™,

fiberglass, GETEK {a blend of polypropylene oxide and fiberglass), etc. .), polysaccharides, nylon or
nitrocellulose, resins, ceramics, mica, silica or silica-based materials including silicon and modified
silicon, carbon, metals, inorganic glasses, and a variety of other polymers.

10 In general, preferred materials include printed circuit board materials. Circuit board materials are

those that comprise an insulating substrate that is coated with a conducting layer and processed using
lithography techniques, particularly photolithography techniques, to form the patterns of electrodes and
interconnects (sometimes referred to in the art as interconnections or leads). The insulating substrate
is generally, but not always, a polymer. As is known in the art, one or a plurality of layers may be used,

15 to make either "two dimensional" (e.g. all electrodes and interconnections in a plane) or "three

dimensional" (wherein the electrodes are on one surface and the interconnects may go through the
board to the other side) boards. Three dimensional systems frequently rely on the use of drilling or
etching, followed by electroplating with a metal such as copper, such that the "through board"
interconnections are made. Circuit board materials are often provided with a foil already attached to

20 the substrate, such as a copper foil, with additional copper added as needed (for example for

interconnections), for example by electroplating. The copper surface may then need to be roughened,
for example through etching, to allow attachment of the adhesion layer.

The substrates comprise one or more metallic surfaces, preferably electrodes. By "metallic surface" or
25 other grammatical equivalents herein is meant any material that can be modified to contain discrete
individual sites appropriate for the attachment or association of target analytes. Preferred metallic
surfaces include, but are not limited to, gold, indium tin oxide, and electrodes.

In a preferred embodiment, the metallic surface is an electrode. By "electrode" herein is meant a
30 composition, which, when connected to an electronic device, is able to sense a current or charge and

convert it to a signal. Thus, an electrode is an ETM as described herein. Preferred electrodes are

known in the art and include, but are not limited to, certain metals and their oxides, including gold;

platinum; palladium; silicon; aluminum; metal oxide electrodes including platinum oxide, titanium oxide,

tin oxide, indium tin oxide, palladium oxide, silicon oxide, aluminum oxide, molybdenum oxide
35 (Mo 2 0 6 ), tungsten oxide (W0 3 ) and ruthenium oxides; and carbon (including glassy carbon electrodes,

graphite and carbon paste). Preferred electrodes include gold, silicon, carbon and metal oxide

electrodes, with gold being particularly preferred.

- 12 -

The substrate may also include arrays, i.e. wherein there is a matrix of addressable detection
electrodes (herein generally referred to "pads", "addresses" or "micro-locations"). By "array" herein is
meant a plurality of capture ligands in an array format; the size of the array will depend on the
composition and end use of the array. Arrays containing from about 2 different capture ligands to

5 many thousands can be made. Generally, the array will comprise from two to as many as 100,000 or
more, depending on the size of the electrodes, as well as the end use of the array. Preferred ranges
are from about 2 to about 10,000, with from about 5 to about 1000 being preferred, and from about 10
to about 100 being particularly preferred. In some embodiments, the compositions of the invention
may not be in array format; that is, for some embodiments, compositions comprising a single capture

10 ligand may be made as well. In addition, in some arrays, multiple substrates may be used, either of
different or identical compositions. Thus for example, large arrays may comprise a plurality of smaller
substrates.

The electrodes described herein are depicted as a flat surface, which is only one of the possible
1 5 conformations of the electrode and is for schematic purposes only. The conformation of the electrode
will vary with the detection method used. For example, flat planar electrodes may be preferred for
optical detection methods, or when arrays of nucleic acids are made, thus requiring addressable
locations for both synthesis and detection. Alternatively, for single probe analysis, the electrode may
be in the form of a tube, with the SAMs comprising AMFS and nucleic acids bound to the inner
20 surface. This allows a maximum of surface area containing the nucleic acids to be exposed to a small
volume of sample.

The electrode comprises asymmetric monolayer forming species. By "monolayer" or "self-assembled
monolayer" or "SAM" herein is meant a relatively ordered assembly of molecules spontaneously

25 chemisorbed on a surface, in which the molecules are oriented approximately parallel to each other
and roughly perpendicular to the surface. Each of the molecules includes a functional group that
adheres to the surface, and a portion that interacts with neighboring molecules in the monolayer to
form the relatively ordered array. A "mixed" monolayer comprises a heterogeneous monolayer, that is,
where at least two different molecules make up the monolayer. As outlined herein, the use of a

30 monolayer reduces the amount of non-specific binding of biomolecules to the surface, and, in the case
of nucleic acids, increases the efficiency of oligonucleotide hybridization as a result of the distance of
the oligonucleotide from the electrode. Thus, a monolayer facilitates the maintenance of the target
analyte away from the electrode surface. In addition, a monolayer serves to keep charge carriers away
from the surface of the electrode. Thus, this layer helps to prevent electrical contact between the

35 electrodes and the ETMs, or between the electrode and charged species within the solvent. Such
contact can result in a direct "short circuit" or an indirect short circuit via charged species which may
be present in the sample. Accordingly, the monolayer is preferably tightly packed in a uniform layer on

- 13 -

the electrode surface, such that a minimum of "holes" exist. The monolayer thus serves as a physical
barrier to block solvent accessibility to the electrode.

In a preferred embodiment, the AMFS comprises a standard monolayer forming species comprises a
5 standard monolayer forming species. By standard monolayer forming species herein is meant an alkyl
chain, preferably linear, from about 7 to 20 carbons in length.

In a preferred embodiment, the AFMS comprise insulator moieties. By "insulator" herein is meant a
substantially nonconducting oligomer, preferably linear. By "substantially nonconducting" herein is
1 0 meant that the insulator will not transfer electrons at or above 1 00 Hz when an AC voltage is applied.
The rate of electron transfer through the insulator is preferably slower than the rate through the
conductive oligomers described herein.

In a preferred embodiment, the insulators have a conductivity, S, of about 10' 7 Q- 1 crrr 1 or lower, with
15 less than about 10 -8 Q" 1 cm 1 being preferred. See generally Gardner et al., supra.

Generally, insulators are alkyl or heteroalkyl oligomers or moieties with sigma bonds, although any
particular insulator molecule may contain aromatic groups or one or more conjugated bonds. By
"heteroalkyl" herein is meant an alkyl group that has at least one heteroatom, i.e. nitrogen, oxygen,
20 sulfur, phosphorus, silicon or boron included in the chain. Alternatively, the insulator may be quite

similar to a conductive oligomer with the addition of one or more heteroatoms or bonds that serve to
inhibit or slow, preferably substantially, electron transfer.

Suitable insulators are known in the art, and include, but are not limited to, -(CH 2 ) n -, -(CRH) n -, and -
25 (CR 2 ) n - ethylene glycol or derivatives using other heteroatoms in place of oxygen, i.e. nitrogen or
sulfur (sulfur derivatives are not preferred when the electrode is gold).

The insulators may be substituted with R groups as defined below to alter the packing of the moieties
or conductive oligomers on an electrode, the hydrophilicity or hydrophobicity of the insulator, and the
30 flexibility, i.e. the rotational, torsional or longitudinal flexibility of the insulator. For example, branched
alkyl groups may be used. Similarly, the insulators may contain terminal groups, as outlined above,
particularly to influence the surface of the monolayer.

The length of the insulator may vary. Preferably the insulator is a straight chain alkyl group,
35 comprising (CH 2 ) n and (OCH 2 CH 2 ) n groups and a terminal OH group. The integer, n, will vary, but
generally will be from about 7 to 20 for (CH 2 ) n and from about 0 to 10 for (OCH 2 CH 2 ) n .

- 14-

In a preferred embodiment, the asymmetric monolayer forming species comprises a disulfide group
which links a monolayer forming species, such as an insulator, and an asymmetric group. Preferably,
the asymmetric group is an electroconduit forming species (EFS). By "electroconduit-forming species"
or "EFS" herein is meant a molecule that is capable of generating sufficient electroconduits in a

5 monolayer, generally of insulators such as alky I groups, to allow detection of ETMs at the surface. In
general, EFS have one or more of the following qualities: they may be relatively rigid molecules, for
example as compared to an alkyl chain; they may attach to the electrode surface with a geometry
different from the other monolayer forming species (for example, alkyl chains attached to gold
surfaces with thiol groups are thought to attach at roughly 45° angles, and phenyl-acetylene chains

10 attached to gold via thiols are thought to go down at 90° angles); they may have a structure that

sterically interferes or interrupts the formation of a tightly packed monolayer, for example through the
inclusion of branching groups such as alkyl groups, or the inclusion of highly flexible species, such as
polyethylene glycol units; or they may be capable of being activated to form electroconduits; for
example, photoactivatible species that can be selectively removed from the surface upon

15 photoactivation, leaving electroconduits.

Preferred EFS include conductive oligomers, as defined below, and phenyl-acetylene-polyethylene
glycol species, and branched alkyl groups.

20 In a preferred embodiment, the EFS is an alkyl group as defined below. If the EFS is a straight chain
alkyl group, 1 to 6 carbon atoms are preferred.

In a preferred embodiment, the EFS is a branched chain alkyl group, substituted with one or more
substitution moieties "R" as defined below. It may be branched at one or more positions. The EFS
25 may be directly attached to an attachment linker as defined below. Alternatively, the EFS may be
attached to the attachment linker via a (CH 2 ) n group, wherein n is an integer from 1 to 4.

In one embodiment, the AFMS has the structure depicted in Structure 44:

30 Structure 44

EFS S S 1

35 In Structure 44, 1 represents an insulator moiety as defined within, EFS is an electroconduit moiety as
defined within and S represents a S atom.

- 15 -

In a preferred embodiment, the AFMS has the structure depicted in Structure 45:

Structure 45

OH

(OCH 2 CH 2 ) m

(CH 2 ) n

(CH 2 ) 0

In this embodiment, n is an integer from 7-16, m is an integer from 0-7 and o is an integer from 0 to 4.
In Structure 45, R1 , R2 and R3 may each be independently selected from the group consisting of
hydrogen, alkyl groups including cycloalkyl, alchol groups, amine groups, amido, ester, phosphorus
moieties, and aryl groups including substituted aryl and heteroaryl.

In a preferred embodiment, the AFMS has the structure depicted in Structure 46:

Structure 46

OH

(OCH 2 CH 2 ) 3

(CH 2 )nCH 3 C

-CH,

In a preferred embodiment, the AFMS has the structure depicted in Structure 47:

Structure 47

OH

(OCH 2 CH 2 ) 3

OH

CHj C CH 3

(CH 2)11 CH2
S S

- 16 -

In one embodiment, in addition to the AFMS, the monolayer comprises insulators.

In one embodiment, in addition to the AFMS, the monolayer comprises conductive oligomers. By
"conductive oligomer" herein is meant a substantially conducting oligomer, preferably linear, some

5 embodiments of which are referred to in the literature as "molecular wires". By "substantially

conducting" herein is meant that the oligomer is capable of transfering electrons at 100 Hz. Generally,
the conductive oligomer has substantially overlapping rr-orbitals, i.e. conjugated n-orbitals, as between
the monomeric units of the conductive oligomer, although the conductive oligomer may also contain
one or more sigma (a) bonds. Additionally, a conductive oligomer may be defined functionally by its

1 0 ability to inject or receive electrons into or from an associated ETM. Furthermore, the conductive
oligomer is more conductive than the insulators as defined herein. Additionally, the conductive
oligomers of the invention are to be distinguished from electroactive polymers, that themselves may
donate or accept electrons.

15 In a preferred embodiment, the conductive oligomers have a conductivity, S, of from between about
10" 6 to about 10 4 Q- 1 crrr 1 , with from about 10" 5 to about 10 3 Q- 1 crrv 1 being preferred, with these S
values being calculated for molecules ranging from about 20A to about 200A. As described below,
insulators have a conductivity S of about 10~ 7 n" 1 cnr 1 or lower, with less than about 10 8 Q" 1 cm 1 being
preferred. See generally Gardner et al., Sensors and Actuators A 51 (1995) 57-66, incorporated

20 herein by reference.

Desired characteristics of a conductive oligomer include high conductivity, sufficient solubility in
organic solvents and/or water for synthesis and use of the compositions of the invention, and
preferably chemical resistance to reactions that occur i) during nucleic acid synthesis (such that
25 nucleosides containing the conductive oligomers may be added to a nucleic acid synthesizer during

the synthesis of the compositions of the invention), ii) during the attachment of the conductive oligomer
to an electrode, or iti) during hybridization assays. In addition, conductive oligomers that will promote
the formation of self-assembled monolayers are preferred.

30 The oligomers of the invention comprise at least two monomeric subunits, as described herein. As is
described more fully below, oligomers include homo- and hetero-oligomers, and include polymers.

In a preferred embodiment, the conductive oligomer has the structure depicted in Structure 1:

Structure 1

- 17-

As will be understood by those in the art, all of the structures depicted herein may have additional
atoms or structures; i.e. the conductive oligomer of Structure 1 may be attached to ETMs, such as
electrodes, transition metal complexes, organic ETMs, and metallocenes, and to nucleic acids, or to
several of these. Unless otherwise noted, the conductive oligomers depicted herein will be attached at
5 the left side to an electrode; that is, as depicted in Structure 1 , the left "Y" is connected to the electrode
as described herein. If the conductive oligomer is to be attached to a nucleic acid, the right "Y", if
present, is attached to the nucleic acid, either directly or through the use of a linker, as is described
herein.

10 In this embodiment, Y is an aromatic group, n is an integer from 1 to 50, g is either 1 or zero, e is an
integer from zero to 10, and m is zero or 1 . When g is 1 , B-D is a bond able to conjugate with
neighboring bonds (herein referred to as a "conjugated bond"), preferably selected from acetylene, B-
D is a conjugated bond, preferably selected from acetylene, alkene, substituted alkene, amide, azo, -
C=N- (including -N=C-, -CR=N- and -N=CR-), -Si=Si-, and -Si=C- (including -C=Si-, -Si=CR- and -

15 CR=Si-). When g is zero, e is preferably 1, D is preferably carbonyl, or a heteroatom moiety, wherein
the heteroatom is selected from oxygen, sulfur, nitrogen, silicon or phosphorus. Thus, suitable
heteroatom moieties include, but are not limited to, -NH and -NR, wherein R is as defined herein;
substituted sulfur; sulfonyl (-S0 2 -) sulfoxide (-SO-); phosphine oxide (-PO- and -RPO-); and
thiophosphine (-PS- and -RPS-). However, when the conductive oligomer is to be attached to a gold

20 electrode, as outlined below, sulfur derivatives are not preferred.

By "aromatic group" or grammatical equivalents herein is meant an aromatic monocyclic or polycyclic
hydrocarbon moiety generally containing 5 to 14 carbon atoms (although larger polycyclic rings
structures may be made) and any carbocylic ketone orthioketone derivative thereof, wherein the

25 carbon atom with the free valence is a member of an aromatic ring. Aromatic groups include arylene
groups and aromatic groups with more than two atoms removed. For the purposes of this application
aromatic includes heterocycle. "Heterocycle" or "heteroaryl" means an aromatic group wherein 1 to 5
of the indicated carbon atoms are replaced by a heteroatom chosen from nitrogen, oxygen, sulfur,
phosphorus, boron and silicon wherein the atom with the free valence is a member of an aromatic ring,

30 and any heterocyclic ketone and thioketone derivative thereof. Thus, heterocycle includes thienyl,
furyl, pyrrolyl, pyrimidinyl, oxalyl, indolyl, purinyl, quinolyl, isoquinolyl, thiazolyl, imidozyl, etc.

Importantly, the Y aromatic groups of the conductive oligomer may be different, i.e. the conductive
oligomer may be a heterooligomer. That is, a conductive oligomer may comprise a oligomer of a
35 single type of Y groups, or of multiple types of Y groups.

- 18-

The aromatic group may be substituted with a substitution group, generally depicted herein as R. R
groups may be added as necessary to affect the packing of the conductive oligomers, i.e. R groups
may be used to alter the association of the oligomers in the monolayer. R groups may also be added
to 1 ) alter the solubility of the oligomer or of compositions containing the oligomers; 2) alter the
conjugation or electrochemical potential of the system; and 3) alter the charge or characteristics at the
surface of the monolayer.

In a preferred embodiment, when the conductive oligomer is greater than three subunits, R groups are
preferred to increase solubility when solution synthesis is done. However, the R groups, and their
positions, are chosen to minimally effect the packing of the conductive oligomers on a surface,
particularly within a monolayer, as described below. In general, only small R groups are used within
the monolayer, with larger R groups generally above the surface of the monolayer. Thus for example
the attachment of methyl groups to the portion of the conductive oligomer within the monolayer to
increase solubility is preferred, with attachment of longer alkoxy groups, for example, C3 to C10, is
preferably done above the monolayer surface. In general, for the systems described herein, this
generally means that attachment of sterically significant R groups is not done on any of the first two or
three oligomer subunits, depending on the average length of the molecules making up the monolayer.

Suitable R groups include, but are not limited to, hydrogen, alkyl, alcohol, aromatic, amino, amido,
nitro, ethers, esters, aldehydes, sulfonyl, silicon moieties, halogens, sulfur containing moieties,
phosphorus containing moieties, and ethylene glycols. In the structures depicted herein, R is
hydrogen when the position is unsubstituted. It should be noted that some positions may allow two
substitution groups, R and R', in which case the R and R' groups may be either the same or different.

By "alkyl group" or grammatical equivalents herein is meant a straight or branched chain alkyl group,
with straight chain alkyl groups being preferred. If branched, it may be branched at one or more
positions, and unless specified, at any position. The alkyl group may range from about 1 to about 30
carbon atoms (C1 -C30), with a preferred embodiment utilizing from about 1 to about 20 carbon atoms
(C1 -C20), with about C1 through about C12 to about C15 being preferred, and C1 to C5 being
particularly preferred, although in some embodiments the alkyl group may be much larger. Also
included within the definition of an alkyl group are cycloalkyl groups such as C5 and C6 rings, and
heterocyclic rings with nitrogen, oxygen, sulfur or phosphorus. Alkyl also includes heteroalkyl, with
heteroatoms of sulfur, oxygen, nitrogen, and silicone being preferred. Alkyl includes substituted alkyl
groups. By "substituted alkyl group" herein is meant an alkyl group further comprising one or more
substitution moieties "R", as defined above.

- 19 -

By "amino groups" or grammatical equivalents herein is meant -NH 2 , -NHR and -NR 2 groups, with R
being as defined herein.

By "nitro group" herein is meant an -N0 2 group.

5

By "sulfur containing moieties" herein is meant compounds containing sulfur atoms, including but not
limited to, thia- thio- and sulfo- compounds, thiols (-SH and -SR), and sulfides (-RSR-). By
"phosphorus containing moieties" herein is meant compounds containing phosphorus, including, but
not limited to, phosphines and phosphates. By "silicon containing moieties" herein is meant
10 compounds containing silicon.

By "ether" herein is meant an -O-R group. Preferred ethers include alkoxy groups, with -0-(CH 2 ) 2 CH 3
and -0-(CH 2 ) 4 CH 3 being preferred. .

15 By "ester" herein is meant a -COOR group.

By "halogen" herein is meant bromine, iodine, chlorine, or fluorine. Preferred substituted alkyls are
partially or fully halogenated alkyls such as CF 3 , etc.

20 By "aldehyde" herein is meant -RCHO groups.

By "alcohol" herein is meant -OH groups, and alkyl alcohols -ROH.

By "amido" herein is meant -RCONH- or RCONR- groups.

25

By "ethylene glycol" or "(poly)ethylene glycol" herein is meant a -(0-CH 2 -CH 2 ) n - group, although each
carbon atom of the ethylene group may also be singly or doubly substituted, i.e. -{0-CR 2 -CR 2 ) n - with
R as described above. Ethylene glycol derivatives with other heteroatoms in place of oxygen (i.e. -(N-
CH 2 -CH 2 ) n - or -(S-CH 2 -CH 2 ) n -, or with substitution groups) are also preferred.

30

Preferred substitution groups include, but are not limited to, methyl, ethyl, propyl, alkoxy groups such
as -0-(CH 2 ) 2 CH 3 and -0-(CH 2 ) 4 CH 3 and ethylene glycol and derivatives thereof.

Preferred aromatic groups include, but are not limited to, phenyl, naphthyl, naphthalene, anthracene,
35 phenanthroline, pyrole, pyridine, thiophene, porphyrins, and substituted derivatives of each of these,
included fused ring derivatives.

-20-

In the conductive oligomers depicted herein, when g is 1 , B-D is a bond linking two atoms or chemical
moieties. In a preferred embodiment, B-D is a conjugated bond, containing overlapping or conjugated
rr-orbitals.

Preferred B-D bonds are selected from acetylene (-C5C-, also called alkyne or ethyne), alkene (-
CH=CH-, also called ethylene), substituted alkene (-CR=CR-, -CH=CR- and -CR=CH-), amide (-NH-
CO- and -NR-CO- or -CO-NH- and -CO-NR-), azo (-N=N-), esters and thioesters (-CO-O-, -O-CO-, -
CS-O- and -0-CS-) and other conjugated bonds such as (-CH=N-, -CR=N-, -N=CH- and -N=CR-), (-
SiH=SiH-, -SiR=SiH- -SiR=SiH-, and -SiR=SiR-), (-SiH=CH-, -SiR=CH-, -SiH=CR-, -SiR=CR-, -
CH=SiH- -CR=SiH-, -CH=SiR-, and -CR=SiR-). Particularly preferred B-D bonds are acetylene,
alkene, amide, and substituted derivatives of these three, and azo. Especially preferred B-D bonds
are acetylene, alkene and amide. The oligomer components attached to double bonds may be in the
trans or cis conformation, or mixtures. Thus, either B or D may include carbon, nitrogen or silicon.
The substitution groups are as defined as above for R.

When g=0 in the Structure 1 conductive oligomer, e is preferably 1 and the D moiety may be carbonyl
or a heteroatom moiety as defined above.

As above for the Y rings, within any single conductive oligomer, the B-D bonds (or D moieties, when
g=0) may be all the same, or at least one may be different. For example, when m is zero, the terminal
B-D bond may be an amide bond, and the rest of the B-D bonds may be acetylene bonds. Generally,
when amide bonds are present, as few amide bonds as possible are preferable, but in some
embodiments all the B-D bonds are amide bonds. Thus, as outlined above for the Y rings, one type of
B-D bond may be present in the conductive oligomer within a monolayer as described below, and
another type above the monolayer level, for example to give greater flexibility for nucleic acid
hybridization when the nucleic acid is attached via a conductive oligomer.

In the structures depicted herein, n is an integer from 1 to 50, although longer oligomers may also be
used (see for example Schumm et al., Angew. Chem. Int. Ed. Engl. 1994 33(13):1360). Without
being bound by theory, it appears that for efficient hybridization of nucleic acids on a surface, the
hybridization should occur at a distance from the surface, i.e. the kinetics of hybridization increase as
a function of the distance from the surface, particularly for long oligonucleotides of 200 to 300
basepairs. Accordingly, when a nucleic acid is attached via a conductive oligomer, as is more fully
described below, the length of the conductive oligomer is such that the closest nucleotide of the
nucleic acid is positioned from about 6A to about 100A (although distances of up to 500A may be
used) from the electrode surface, with from about 1 5A to about 60A being preferred and from about
25A to about 60A also being preferred. Accordingly, n will depend on the size of the aromatic group,

-21 -

but generally will be from about 1 to about 20, with from about 2 to about 15 being preferred and from
about 3 to about 10 being especially preferred.

In the structures depicted herein, m is either 0 or 1 . That is, when m is 0, the conductive oligomer may
terminate in the B-D bond or D moiety, i.e. the D atom is attached to the nucleic acid either directly or
via a linker. In some embodiments, for example when the conductive oligomer is attached to a
phosphate of the ribose-phosphate backbone of a nucleic acid, there may be additional atoms, such
as a linker, attached between the conductive oligomer and the nucleic acid. Additionally, as outlined
below, the D atom may be the nitrogen atom of the ami no-modified ribose. Alternatively, when m is 1 ,
the conductive oligomer may terminate in Y, an aromatic group, i.e. the aromatic group is attached to
the nucleic acid or linker.

As will be appreciated by those in the art, a large number of possible conductive oligomers may be
utilized. These include conductive oligomers falling within the Structure 1 and Structure 8 formulas, as
well as other conductive oligomers, as are generally known in the art, including for example,
compounds comprising fused aromatic rings or Teflon<EMike oligomers, such as -(CF 2 ) n -, -(CHF) n - and
-(CFR) n -. See for example, Schumm etal., Angew. Chem. Intl. Ed. Engl. 33:1361 (1994);Grosshenny
et al., Platinum Metals Rev. 40(1):26-35 (1996); Tour, Chem. Rev. 96:537-553 (1996); Hsung et al.,
Organometallics 14:4808-4815 (1995; and references cited therein, all of which are expressly
incorporated by reference.

Particularly preferred conductive oligomers of this embodiment are depicted below:

Structure 2 is Structure 1 when g is 1 . Preferred embodiments of Structure 2 include: e is zero, Y is
pyrole or substituted pyrole; e is zero, Y is thiophene or substituted thiophene; e is zero, Y is furan or
substituted furan; e is zero, Y is phenyl or substituted phenyl; e is zero, Y is pyridine or substituted
pyridine; e is 1, B-D is acetylene and Y is phenyl or substituted phenyl (see Structure 4 below). A
preferred embodiment of Structure 2 is also when e is one, depicted as Structure 3 below:

Structure 2

Structure 3

-22-

Preferred embodiments of Structure 3 are: Y is phenyl or substituted phenyl and B-D is azo; Y is
phenyl or substituted phenyl and B-D is acetylene; Y is phenyl or substituted phenyl and B-D is alkene;
Y is pyridine or substituted pyridine and B-D is acetylene; Y is thiophene or substituted thiophene and
B-D is acetylene; Y is furan or substituted furan and B-D is acetylene; Y is thiophene or furan (or
substituted thiophene or furan) and B-D are alternating alkene and acetylene bonds.

Most of the structures depicted herein utilize a Structure 3 conductive oligomer. However, any
Structure 3 oligomers may be substituted with any of the other structures depicted herein, i.e.
Structure 1 or 8 oligomer, or other conducting oligomer, and the use of such Structure 3 depiction is
not meant to limit the scope of the invention.

Particularly preferred embodiments of Structure 3 include Structures 4, 5, 6 and 7, depicted below:

Structure 4

Particularly preferred embodiments of Structure 4 include: n is two, m is one, and R is hydrogen; n is
three, m is zero, and R is hydrogen; and the use of R groups to increase solubility.

Structure 5

When the B-D bond is an amide bond, as in Structure 5, the conductive oligomers are pseudopeptide
oligomers. Although the amide bond in Structure 5 is depicted with the carbonyl to the left, i.e. -
CONH-, the reverse may also be used, i.e. -NHCO-. Particularly preferred embodiments of Structure
5 include: n is two, m is one, and R is hydrogen; n is three, m is zero, and R is hydrogen (in this
embodiment, the terminal nitrogen (the D atom) may be the nitrogen of the ami no-modified ribose);
and the use of R groups to increase solubility.

Structure 6

Preferred embodiments of Structure 6 include the first n is two, second n is one, m is zero, and all R
groups are hydrogen, or the use of R groups to increase solubility.

-23-

Structure 7

5

Preferred embodiments of Structure 7 include: the first n is three, the second n is from 1-3, with m
being either 0 or 1 , and the use of R groups to increase solubility.

In a preferred embodiment, the conductive oligomer has the structure depicted in Structure 8:
10 Structure8

in this embodiment, C are carbon atoms, n is an integer from 1 to 50, m is 0 or 1, J is a heteroatom
15 selected from the group consisting of oxygen, nitrogen, silicon, phosphorus, sulfur, carbonyl or

sulfoxide, and G is a bond selected from alkane, alkene or acetylene, such that together with the two
carbon atoms the C-G-C group is an alkene (-CH=CH-), substituted alkene (-CR=CR-) or mixtures
thereof (-CH=CR- or -CR=CH-), acetylene (-C^C-), or alkane (-CR 2 -CR 2 -, with R being either
hydrogen or a substitution group as described herein). The G bond of each subunit may be the same
20 or different than the G bonds of other subunits; that is, alternating oligomers of alkene and acetylene
bonds could be used, etc. However, when G is an alkane bond, the number of alkane bonds in the
oligomer should be kept to a minimum, with about six or less sigma bonds per conductive oligomer
being preferred. Alkene bonds are preferred, and are generally depicted herein, although alkane and
acetylene bonds may be substituted in any structure or embodiment described herein as will be
25 appreciated by those in the art.

In some embodiments, for example when ETMs are not present, if m=0 then at least one of the G
bonds is not an alkane bond.

30 In a preferred embodiment, the m of Structure 8 is zero. In a particularly preferred embodiment, m is
zero and G is an alkene bond, as is depicted in Structure 9:

Structure 9

R

35

-24 -

The alkene oligomer of structure 9, and others depicted herein, are generally depicted in the preferred
trans configuration, although oligomers of cis or mixtures of trans and cis may also be used. As
above, R groups may be added to alter the packing of the compositions on an electrode, the
hydrophilicity or hydrophobicity of the oligomer, and the flexibility, i.e. the rotational, torsional or
longitudinal flexibility of the oligomer, n is as defined above.

In a preferred embodiment, R is hydrogen, although R may be also alky! groups and polyethylene
glycols or derivatives.

In an alternative embodiment, the conductive oligomer may be a mixture of different types of
oligomers, for example of structures 1 and 8.

In addition, the terminus of at least some of the conductive oligomers in the monolayer are
electronically exposed. By "electronically exposed" herein is meant that upon the placement of an
ETM in close proximity to the terminus, and after initiation with the appropriate signal, a signal
dependent on the presence of the ETM may be detected. The conductive oligomers may or may not
have terminal groups. Thus, in a preferred embodiment, there is no additional terminal group, and the
conductive oligomer terminates with one of the groups depicted in Structures 1 to 9; for example, a B-
D bond such as an acetylene bond. Alternatively, in a preferred embodiment, a terminal group is
added, sometimes depicted herein as "Q". A terminal group may be used for several reasons; for
example, to contribute to the electronic availability of the conductive oligomer for detection of ETMs, or
to alter the surface of the SAM for other reasons, for example to prevent non-specific binding. For
example, there may be negatively charged groups on the terminus to form a negatively charged
surface such that when the nucleic acid is DNA or RNA the nucleic acid is repelled or prevented from
lying down on the surface, to facilitate hybridization. Preferred terminal groups include -NH 2 , -OH, -
COOH, and alkyl groups such as -CH 3 , and (poly)alkyloxides such as (poly)ethylene glycol, with -
OCH 2 CH 2 OH, -(OCH 2 CH 2 0) 2 H, -(OCH 2 CH 2 0) 3 H, and -(OCH 2 CH 2 0) 4 H being preferred.

In one embodiment, it is possible to use mixtures of conductive oligomers with different types of
terminal groups. Thus, for example, some of the terminal groups may facilitate detection, and some
may prevent non-specific binding.

It will be appreciated that the monolayer may comprise different conductive oligomer species, although
preferably the different species are chosen such that a reasonably uniform SAM can be formed. Thus,
for example, when nucleic acids are covalently attached to the electrode using conductive oligomers, it
is possible to have one type of conductive oligomer used to attach the nucleic acid, and another type
functioning to detect the ETM. Similarly, it may be desirable to have mixtures of different lengths of

-25-

conductive oligomers in the monolayer, to help reduce non-specific signals. Thus, for example,
preferred embodiments utilize conductive oligomers that terminate below the surface of the rest of the
monolayer, i.e. below the insulator layer, if used, or below some fraction of the other conductive
oligomers. Similarly, the use of different conductive oligomers may be done to facilitate monolayer
formation, or to make monolayers with altered properties.

The length of the species making up the monolayer will vary as needed. As outlined above, it appears
that binding is more efficient at a distance from the surface. The species to which capture binding
ligands are attached (as outlined below, these can be either insulators or conductive oligomers) may
be basically the same length as the monolayer forming species or longer than them, resulting in the
nucleic acids being more accessible to the solvent for hybridization. In some embodiments, the
conductive oligomers to which the capture binding ligands are attached may be shorter than the
monolayer.

The covalent attachment of the conductive oligomers and insulators may be accomplished in a variety
of ways, depending on the electrode and the composition of the insulators and conductive oligomers
used. In a preferred embodiment, the attachment linkers with covalently attached capture binding
ligands as depicted herein are covalently attached to an electrode. Thus, one end or terminus of the
attachment linker is attached to the capture binding ligand, and the other is attached to an electrode.
In some embodiments it may be desirable to have the attachment linker attached at a position other
than a terminus, or even to have a branched attachment linker that is attached to an electrode at one
terminus and to two or more capture binding ligands at other termini, although this is not preferred.
Similarly, the attachment linker may be attached at two sites to the electrode, as is generally depicted
in Structures 11-13. Generally, some type of linker is used, as depicted below as "A" in Structure 10,
where "X" is the conductive oligomer, "I" is an insulator and the hatched surface is the electrode:

In this embodiment, A is a linker or atom. The choice of "A" will depend in part on the characteristics
of the electrode. Thus, for example, A may be a sulfur moiety when a gold electrode is used.
Alternatively, when metal oxide electrodes are used, A may be a silicon (silane) moiety attached to the
oxygen of the oxide (see for example Chen et al., Langmuir 10:3332-3337 (1994); Lenhard et al., J.
Electroanal. Chem. 78:195-201 (1977), both of which are expressly incorporated by reference). When

Structure 1 0

-26 -

carbon based electrodes are used, A may be an amino moiety (preferably a primary amine; see for
example Deinhammeretal., Langmuir 10:1306-1313 (1994)). Thus, preferred A moieties include, but
are not limited to, silane moieties, sulfur moieties (including alkyl sulfur moieties), and amino moieties.
In a preferred embodiment, epoxide type linkages with redox polymers such as are known in the art
5 are not used.

Although depicted herein as a single moiety, the insulators and conductive oligomers may be attached
to the electrode with more than one "A" moiety; the "A" moieties may be the same or different. Thus,
for example, when the electrode is a gold electrode, and "A" is a sulfur atom or moiety, multiple sulfur
10 atoms may be used to attach the conductive oligomer to the electrode, such as is generally depicted
below in Structures 1 1 , 12 and 13. As will be appreciated by those in the art, other such structures
can be made. In Structures 11, 12 and 13, the A moiety is just a sulfur atom, but substituted sulfur
moieties may also be used.

Structure 1 1

15

20 Structure 12

25

30

It should also be noted that similar to Structure 13, it may be possible to have a conductive oligomer
terminating in a single carbon atom with three sulfur moities attached to the electrode. Additionally,
35 although not always depicted herein, the conductive oligomers and insulators may also comprise a "Q"
terminal group.

-27-

In a preferred embodiment, the electrode is a gold electrode, and attachment is via a sulfur linkage as
is well known in the art, i.e. the A moiety is a sulfur atom or moiety. Although the exact characteristics
of the gold-sulfur attachment are not known, this linkage is considered covalent for the purposes of
this invention. Representative structures are depicted in Structure 14 and Structure 48. Structure 14
uses the Structure 3 conductive oligomer, although as for all the structures depicted herein, any of the
conductive oligomers, or combinations of conductive oligomers, may be used. Similarly, any of the
conductive oligomers or insulators may also comprise terminal groups as described herein. Structure
14 depicts the "A" linker as comprising just a sulfur atom, although additional atoms may be present
(i.e. linkers from the sulfur to the conductive oligomer or substitution groups).

Structure 14

Structure 48 depicts the "A" linker as comprising a cyclic disulfide to which an insulator (I) is attached.
Preferably the insulator is a standard monolayer forming species as defined herein, although as will be
appreciated by those of skill in the art, other insulators as are known in the art and conductive
oligomer may be used as well.

Structure 48

In a preferred embodiment, the electrode is a carbon electrode, i.e. a glassy carbon electrode, and
attachment is via a nitrogen of an amine group. A representative structure is depicted in Structure 15.
Again, additional atoms may be present, i.e. Z type linkers and/or terminal groups.

Structure 1 5

-28-

Structure 16

In Structure 16, the oxygen atom is from the oxide of the metal oxide electrode. The Si atom may also
contain other atoms, i.e. be a silicon moiety containing substitution groups. Other attachments for
SAMs to other electrodes are known in the art; see for example Napier et al., Langmuir, 1997, for
attachment to indium tin oxide electrodes, and also the chemisorption of phosphates to an indium tin
oxide electrode (talk by H. Holden Thorpe, CHI conference, May 4-5, 1998).

As will be appreciated by those in the art, the actual combinations and ratios of the different species
making up the monolayer can vary widely. Generally, three component systems are preferred, with
the first species comprising a capture binding ligand containing species (i.e. a capture probe, that can
be attached to the electrode via either an insulator or a conductive oligomer, as is more fully described
below). The second species are the insulators, and the third species are electroconduit forming
species. In this embodiment, the first species can comprise from about 90% to about 1%, with from
about 20% to about 40% being preferred. When the capture binding ligands are nucleic acids and the
target is nucleic acid as well, from about 30% to about 40% is especially preferred for short
oligonucleotide targets and from about 10% to about 20% is preferred for longer targets. The second
species can comprise from about 1% to about 90%, with from about 20% to about 90% being
preferred, and from about 40% to about 60% being especially preferred. The third species can
comprise from about 1% to about 90%, with from about 20% to about 40% being preferred, and from
about 15% to about 30% being especially preferred. Preferred ratios of first:second:third species are
2:2:1 for short targets, 1:3:1 for longer targets, with total thiol concentration in the 500 uM to 1 mM
range, and 833 uM being preferred.

In a preferred embodiment, two component systems are used, comprising the first and second
species. In this embodiment, the first species can comprise from about 90% to about 1%, with from
about 1% to about 40% being preferred, and from about 10% to about 40% being especially preferred.
The second species can comprise from about 1% to about 90%, with from about 10% to about 60%
being preferred, and from about 20% to about 40% being especially preferred.

In a particularly preferred embodiment, two component systems are used, comprising the first species
and wherein the second species is the AFMS. In this embodiment, the first species can comprise from
about 90% to about 1%, with from about 1% to about 40% being preferred, and from about 10% to

-29-

about 40% being especially preferred. The second species, the AFMS, can comprise from about 1%
to about 90%, with from about 10% to about 60% being preferred, and from about 20% to about 40%
being especially preferred.

5 In a particularly preferred embodiment, the aqueous solution used to form the monolayer also

comprises s a pH buffering component and a zwitterionic hygroscopic agent. Preferably the buffer is
Tris and the hygroscopic agent is betaine. Prefereable, the concentartion of the buffer is about 1 mlVI
to1 M and more preferable about 10 mM to about 200 mM. Also preferable, the concentration of the
hygroscopic agent is from about 1 mM to about 1M and more preferably from about 100 mM to about
10 800 mM.

The SAMs of the invention can be made in a variety of ways, including deposition out of organic
solutions and deposition out of aqueous solutions. The methods outlined herein use a gold electrode
as the example, although as will be appreciated by those in the art, other metals and methods may be
15 used as well. In one preferred embodiment, indium-tin-oxide (ITO) is used as the electrode.

In a preferred embodiment, a gold surface is first cleaned. A variety of cleaning procedures may be
employed, including, but not limited to, chemical cleaning or etchants (including Piranha solution
(hydrogen peroxide/sulfuric acid) or aqua regia (hydrochloric acid/nitric acid), electrochemical
20 methods, flame treatment, plasma treatment or combinations thereof.

In a particularly preferred embodiment, the SAM is formed in only one step and the second step is
omitted.

25 Following cleaning, the gold substrate is exposed to the SAM species. When the electrode is ITO, the
SAM species are phosphonate-containing species. This can also be done in a variety of ways,
including, but not limited to, solution deposition, gas phase deposition, microcontact printing, spray
deposition, deposition using neat components, etc. A preferred embodiment utilizes a deposition
solution comprising a mixture of various SAM species in solution, generally thiol-containing species.

30 Mixed monolayers that contain nucleic acids are usually prepared using a two step procedure. The
thioiated nucleic acid is deposited during the first deposition step (generally in the presence of at least
one other monolayer-forming species) and the mixed monolayer formation is completed during the
second step in which a second thiol solution minus nucleic acid is added. The second step frequently
involves mild heating to promote monolayer reorganization.

35

In a preferred embodiment, the deposition solution is an organic deposition solution. In this
embodiment, a clean gold surface is placed into a clean vial. A binding ligand deposition solution in

-30-

organic solvent is prepared in which the total thiol concentration is between micromolarto saturation;
preferred ranges include from about 1 uM to 10 mM, with from about 400 uM to about 1.0 mM being
especially preferred. In a preferred embodiment, the deposition solution contains thiol modified DNA
(i.e. nucleic acid attached to an attachment linker) and thiol diluent molecules (either conductive
5 oligomers or insulators, with the latter being preferred). The ratio of nucleic acid to diluent (if present)
is usually between 1000:1 to 1:1000, with from about 10:1 to about 1:10 being preferred and 1:1 being
especially preferred. The preferred solvents are tetrahydrofuran (THF), acetonitrile, dimethylforamide
(DMF), ethanol, or mixtures thereof; generally any solvent of sufficient polarity to dissolve the capture
ligand can be used, as long as the solvent is devoid of functional groups that will react with the

10 surface. Sufficient nucleic acid deposition solution is added to the vial so as to completely cover the
electrode surface. The gold substrate is allowed to incubate at ambient temperature or slightly above
ambient temperature for a period of time ranging from seconds to hours, with 5-30 minutes being
preferred. After the initial incubation, the deposition solution is removed and a solution of diluent
molecule only (from about 1 uM to 10 mM, with from about 100 uM to about 1.0 mM being preferred)

15 in organic solvent is added. The gold substrate is allowed to incubate at room temperature or above
room temperature for a period of time (seconds to days, with from about 10 minutes to about 24 hours
being preferred). The gold sample is removed from the solution, rinsed in clean solvent and used.

In a preferred embodiment, an aqueous deposition solution is used. As above, a clean gold surface is
20 placed into a clean vial. A nucleic acid deposition solution in water is prepared in which the total thiol
concentration is between about 1 uM and 10 mM, with from about 1 uM to about 200 uM being
preferred. The aqueous solution frequently has salt present (up to saturation, with approximately 1M
being preferred), however pure water can be used. The deposition solution contains thiol modified
nucleic acid and often a thiol diluent molecule. The ratio of nucleic acid to diluent is usually between
25 between 1000:1 to 1:1000, with from about 10:1 to about 1:10 being preferred and 1:1 being especially
preferred. The nucleic acid deposition solution is added to the vial in such a volume so as to
completely cover the electrode surface. The gold substrate is allowed to incubate at ambient
temperature or slightly above ambient temperature for 1-30 minutes with 5 minutes usually being
sufficient. After the initial incubation, the deposition solution is removed and a solution of diluent
30 molecule only (1 0 uM -1 .0 mM) in either water or organic solvent is added. The gold substrate is
allowed to incubate at room temperature or above room temperature until a complete monolayer is
formed (10 minutes-24 hours). The gold sample is removed from the solution, rinsed in clean solvent
and used.

35 In a preferred embodiment, the deposition solution comprises a zwitterionic compound, preferably
betaine. Preferred embodiments utilize betain and Tris-HCI buffers.

-31 -

In a preferred embodiment, as outlined herein, a circuit board is used as the substrate for the gold
electrodes. Formation of the SAMs on the gold surface is generally done by first cleaning the boards,
for example in a 10% sulfuric acid solution for 30 seconds, detergent solutions, aqua regia, plasma,
etc., as outlined herein. Following the sulfuric acid treatment, the boards are washed, for example via
5 immersion in two Milli-Q water baths for 1 minute each. The boards are then dried, for example under
a stream of nitrogen. Spotting of the deposition solution onto the boards is done using any number of
known spotting systems, generally by placing the boards on an X-Y table, preferably in a humidity
chamber. The size of the spotting drop will vary with the size of the electrodes on the boards and the
equipment used for delivery of the solution; for example, for 250 uM size electrodes, a 30 nanoliter

1 0 drop is used. The volume should be sufficient to cover the electrode surface completely. The drop is
incubated at room temperature for a period of time (sec to overnight, with 5 minutes preferred) and
then the drop is removed by rinsing in a Milli-Q water bath. The boards are then preferably treated
with a second deposition solution, generally comprising insulator in organic solvent, preferably
acetonitrile, by immersion in a 45°C bath. After 30 minutes, the boards are removed and immersed in

15 an acetonitrile bath for 30 seconds followed by a milli-Q water bath for 30 seconds. The boards are
dried under a stream of nitrogen.

In a preferred embodiment, the electrode comprising the monolayer including conductive oligomers
further comprises a capture binding ligand. By "capture binding ligand" or "capture binding species" or

20 "capture probe" herein is meant a compound that is used to probe for the presence of the target
analyte, that will bind to the target analyte. Generally, the capture binding ligand allows the
attachment of a target analyte to the electrode, for the purposes of detection. As is more fully outlined
below, attachment of the target analyte to the capture probe may be direct (i.e. the target analyte binds
to the capture binding ligand) or indirect (one or more capture extender ligands are used). By

25 "covalently attached" herein is meant that two moieties are attached by at least one bond, including
sigma bonds, pi bonds and coordination bonds.

In a preferred embodiment, the binding is specific, and the binding ligand is part of a binding pair. By
"specifically bind" herein is meant that the ligand binds the analyte, with specificity sufficient to

30 differentiate between the analyte and other components or contaminants of the test sample. However,
as will be appreciated by those in the art, it will be possible to detect analytes using binding which is
not highly specific; for example, the systems may use different binding ligands, for example an array of
different ligands, and detection of any particular analyte is via its "signature" of binding to a panel of
binding ligands, similar to the manner in which "electronic noses" work. This finds particular utility in

35 the detection of chemical analytes. The binding should be sufficient to remain bound under the

conditions of the assay, including wash steps to remove non-specific binding. In some embodiments,
for example in the detection of certain biomolecules, the binding constants of the analyte to the binding

-32-

ligand will be at least about 1 0 4 -1 0 s M" 1 , with at least about 10 s to 10 9 M" 1 being preferred and at least
about 10 7 -10 9 M" 1 being particularly preferred.

As will be appreciated by those in the art, the composition of the binding ligand will depend on the
5 composition of the target analyte. Binding ligands to a wide variety of analytes are known or can be
readily found using known techniques. For example, when the analyte is a single-stranded nucleic
acid, the binding ligand may be a complementary nucleic acid. Similarly, the analyte may be a nucleic
acid binding protein and the capture binding ligand is either single-stranded or double stranded nucleic
acid; alternatively, the binding ligand may be a nucleic acid-binding protein when the analyte is a

10 single or double-stranded nucleic acid. When the analyte is a protein, the binding ligands include

proteins or small molecules. Preferred binding ligand proteins include peptides. For example, when
the analyte is an enzyme, suitable binding ligands include substrates and inhibitors. As will be
appreciated by those in the art, any two molecules that will associate may be used, either as an
analyte or as the binding ligand. Suitable analyte/binding ligand pairs include, but are not limited to,

15 antibodies/antigens, receptors/ligands, proteins/nucleic acid, enzymes/substrates and/or inhibitors,
carbohydrates (including glycoproteins and glycolipids)/lectins, proteins/proteins, proteins/small
molecules; and carbohydrates and their binding partners are also suitable analyte-binding ligand pairs.
These may be wild-type or derivative sequences. In a preferred embodiment, the binding ligands are
portions (particularly the extracellular portions) of cell surface receptors that are known to multimerize,

20 such as the growth hormone receptor, glucose transporters (particularly GLUT 4 receptor), transferrin
receptor, epidermal growth factor receptor, low density lipoprotein receptor, high density lipoprotein
receptor, epidermal growth factor receptor, leptin receptor, interleukin receptors including IL-1, IL-2,
IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-11, IL-12, IL-13, IL-15, and IL-17 receptors, human growth
hormone receptor, VEGF receptor, PDGF receptor, EPO receptor, TPO receptor, ciliary neurotrophic

25 factor receptor, prolactin receptor, and T-cell receptors.

The method of attachment of the capture binding ligand to the attachment linker will generally be done
as is known in the art, and will depend on the composition of the attachment linker and the capture
binding ligand. In general, the capture binding ligands are attached to the attachment linker through

30 the use of functional groups on each that can then be used for attachment. Preferred functional
groups for attachment are amino groups, carboxy groups, oxo groups and thiol groups. These
functional groups can then be attached, either directly or through the use of a linker, sometimes
depicted herein as "Z". Linkers are known in the art; for example, homo-or hetero-bifunctional linkers
as are well known (see 1994 Pierce Chemical Company catalog, technical section on cross-linkers,

35 pages 155-200, incorporated herein by reference). Preferred Z linkers include, but are not limited to,
alkyl groups (including substituted alkyl groups and alkyl groups containing heteroatom moieties), with

-33-

short alkyl groups, esters, amide, amine, epoxy groups and ethylene glycol and derivatives being
preferred. Z may also be a sulfone group, forming sulfonamide.

In this way, capture binding ligands comprising proteins, lectins, nucleic acids, small organic
5 molecules, carbohydrates, etc. can be added.

In a preferred embodiment, the capture binding ligand is attached directly to the electrode as outlined
herein, for example via an attachment linker. Alternatively, the capture binding ligand may utilize a
capture extender component, such as depicted in Figure 7G. In this embodiment, the capture binding
1 0 ligand comprises a first portion that will bind the target analyte and a second portion that can be used
for attachment to the surface. Figure7A-7R depict the use of a nucleic acid component for binding to
the surface, although this can be other binding partners as well.

A preferred embodiment utilizes proteinaceous capture binding ligands. As is known in the art, any
15 number of techniques may be used to attach a proteinaceous capture binding ligand. "Protein" in this
context includes proteins, polypeptides and peptides. A wide variety of techniques are known to add
moieties to proteins. One preferred method is outlined in U.S. Patent No. 5,620,850, hereby
incorporated by reference in its entirety. The attachment of proteins to electrodes is known; see also
Heller, Acc. Chem. Res. 23:128 (1990), and related work.

20

A preferred embodiment utilizes nucleic acids as the capture binding ligand, for example for when the
target analyte is a nucleic acid or a nucleic acid binding protein, or when the nucleic acid serves as an
aptamerfor binding a protein; see U.S. Patents 5,270,163, 5,475,096, 5,567,588, 5,595,877,
5,637,459, 5,683,867,5,705,337, and related patents, hereby incorporated by reference. In this

25 embodiment, the nucleic acid capture binding ligand is covalently attached to the electrode, via an

"attachment linker", that can be either a conductive oligomer or via an insulator. Thus, one end of the
attachment linker is attached to a nucleic acid, and the other end (although as will be appreciated by
those in the art, it need not be the exact terminus for either) is attached to the electrode. Thus, any of
structures 1-16 may further comprise a nucleic acid effectively as a terminal group. Thus, the present

30 invention provides compositions comprising binding ligands covalently attached to electrodes as is
generally depicted below in Structure 17 for a nucleic acid:

Structure 17

35

-(Xorl)

-34-

In Structure 17, the hatched marks on the left represent an electrode. X is a conductive oligomer and I
is an insulator as defined herein. F., is a linkage that allows the covalent attachment of the electrode
and the conductive oligomer or insulator, including bonds, atoms or linkers such as is described
herein, for example as "A", defined below. F 2 is a linkage that allows the covalent attachment of the
5 conductive oligomer or insulator to the binding ligand, a nucleic acid in Structure 17, and may be a

bond, an atom or a linkage as is herein described. F 2 may be part of the conductive oligomer, part of
the insulator, part of the binding ligand, or exogeneous to both, for example, as defined herein for "Z".

In general, the methods, synthetic schemes and compositions useful for the attachment of capture
10 binding ligands, particularly nucleic acids, are outlined in WO98/20162, PCT US98/12430, PCT

US98/12082; PCT US99/01705 and PCT US99/01703, all of which are expressly incorporated herein
by reference in their entirety.

In a preferred embodiment, the capture binding ligand is covalently attached to the electrode via a
1 5 conductive oligomer. The covalent attachment of the binding ligand and the conductive oligomer may
be accomplished in several ways, as will be appreciated by those in the art.

In a preferred embodiment, the capture binding ligand is a nucleic acid, and the attachment is via
attachment to the base of the nucleoside, via attachment to the backbone of the nucleic acid (either
20 the ribose, the phosphate, or to an analogous group of a nucleic acid analog backbone), or via a

transition metal ligand, as described below. The techniques outlined below are generally described for
naturally occuring nucleic acids, although as will be appreciated by those in the art, similar techniques
may be used with nucleic acid analogs.

25 In a preferred embodiment, the conductive oligomer is attached to the base of a nucleoside of the

nucleic acid. This may be done in several ways, depending on the oligomer, as is described below. In
one embodiment, the oligomer is attached to a terminal nucleoside, i.e. either the 3' or 5' nucleoside of
the nucleic acid. Alternatively, the conductive oligomer is attached to an internal nucleoside.

30 The point of attachment to the base will vary with the base. Generally, attachment at any position is
possible. In some embodiments, for example when the probe containing the ETMs may be used for
hybridization, it is preferred to attach at positions not involved in hydrogen bonding to the
complementary base. Thus, for example, generally attachment is to the 5 or 6 position of pyrimidines
such as uridine, cytosine and thymine. For purines such as adenine and guanine, the linkage is

35 preferably via the 8 position. Attachment to non-standard bases is preferably done at the comparable
positions.

-35-

In one embodiment, the attachment is direct; that is, there are no intervening atoms between the
conductive oligomer and the base. In this embodiment, for example, conductive oligomers with
terminal acetylene bonds are attached directly to the base. Structure 18 is an example of this linkage,
using a Structure 3 conductive oligomer and uridine as the base, although other bases and conductive
5 oligomers can be used as will be appreciated by those in the art:

Structure 1 8

o

10

15 It should be noted that the pentose structures depicted herein may have hydrogen, hydroxy,

phosphates or other groups such as amino groups attached. In addition, the pentose and nucleoside
structures depicted herein are depicted non-conventionally, as mirror images of the normal rendering.
In addition, the pentose and nucleoside structures may also contain additional groups, such as
protecting groups, at any position, for example as needed during synthesis.

20'

In addition, the base may contain additional modifications as needed, i.e. the carbonyl or amine groups
may be altered or protected.

In an alternative embodiment, the attachment is any number of different Z linkers, including amide and
25 amine linkages, as is generally depicted in Structure 19 using uridine as the base and a Structure 3
oligomer:

Structure 19:

35

In this embodiment, Z is a linker. Preferably, Z is a short linker of about 1 to about 10 atoms, with from
1 to 5 atoms being preferred, that may or may not contain alkene, alkynyl, amine, amide, azo, imine,

-36-

etc., bonds. Linkers are known in the art; for example, homo-or hetero-bifunctional linkers as are well
known (see 1994 Pierce Chemical Company catalog, technical section on cross-iinkers, pages
155-200, incorporated herein by reference). Preferred Z linkers include, but are not limited to, alkyl
groups (including substituted alkyl groups and alkyl groups containing heteroatom moieties), with short
5 alkyl groups, esters, amide, amine, epoxy groups and ethylene glycol and derivatives being preferred,
with propyl, acetylene, and C 2 alkene being especially preferred. Z may also be a sulfone group,
forming sulfonamide linkages as discussed below.

In a preferred embodiment, the attachment of the nucleic acid and the conductive oligomer is done via
10 attachment to the backbone of the nucleic acid. This may be done in a number of ways, including
attachment to a ribose of the ribose-phosphate backbone, or to the phosphate of the backbone, or
other groups of analogous backbones.

As a preliminary matter, it should be understood that the site of attachment in this embodiment may be
15 to a 3' or 5' terminal nucleotide, or to an internal nucleotide, as is more fully described below.

In a preferred embodiment, the conductive oligomer is attached to the ribose of the ribose-phosphate
backbone. This may be done in several ways. As is known in the art, nucleosides that are modified at
either the 2' or 3' position of the ribose with amino groups, sulfur groups, silicone groups, phosphorus
20 groups, or oxo groups can be made (Imazawa et al., J. Org. Chem., 44:2039 (1979); Hobbs et al., J.
Org. Chem. 42(4):714 (1977); Verheyden et al., J. Orrg. Chem. 36(2):250 (1971); McGee et al., J.
Org. Chem. 61:781-785 (1996); Mikhailopulo et al., Liebigs. Ann. Chem. 513-519 (1993); McGee et
al., Nucleosides & Nucleotides 14(6):1329 (1995), all of which are incorporated by reference). These
modified nucleosides are then used to add the conductive oligomers.

25

A preferred embodiment utilizes amino-modified nucleosides. These amino-modified riboses can then
be used to form either amide or amine linkages to the conductive oligomers. In a preferred
embodiment, the amino group is attached directly to the ribose, although as will be appreciated by
those in the art, short linkers such as those described herein for "Z" may be present between the
30 amino group and the ribose.

In a preferred embodiment, an amide linkage is used for attachment to the ribose. Preferably, if the
conductive oligomer of Structures 1-3 is used, m is zero and thus the conductive oligomer terminates
in the amide bond. In this embodiment, the nitrogen of the amino group of the amino-modified ribose
35 is the "D" atom of the conductive oligomer. Thus, a preferred attachment of this embodiment is
depicted in Structure 20 (using the Structure 3 conductive oligomer):

-37-

Structure 20

0

Y b Dj Y C N-

O

-bas

As wili be appreciated by those in the art, Structure 20 has the terminal bond fixed as an amide bond.

10

15

In a preferred embodiment, a heteroatom linkage is used, i.e. oxo, amine, sulfur, etc. A preferred
embodiment utilizes an amine linkage. Again, as outlined above for the amide linkages, for amine
linkages, the nitrogen of the amino-modified ribose may be the "D" atom of the conductive oligomer
when the Structure 3 conductive oligomer is used. Thus, for example, Structures 21 and 22 depict
nucleosides with the Structures 3 and 9 conductive oligomers, respectively, using the nitrogen as the
heteroatom, athough other heteroatoms can be used:

Structure 21

~( Y-B-, i~^ z ^

bas

20

25

In Structure 21 , preferably both m and t are not zero. A preferred Z here is a methylene group, or
other aliphatic alkyl linkers. One, two or three carbons in this position are particularly useful for
synthetic reasons.

Structure 22

base

In Structure 22, Z is as defined above. Suitable linkers include methylene and ethylene.

In an alternative embodiment, the conductive oligomer is covalently attached to the nucleic acid via the
30 phosphate of the ribose-phosphate backbone (or analog) of a nucleic acid. In this embodiment, the
attachment is direct, utilizes a linker or via an amide bond. Structure 23 depicts a direct linkage, and
Structure 24 depicts linkage via an amide bond (both utilize the Structure 3 conductive oligomer,
although Structure 8 conductive oligomers are also possible). Structures 23 and 24 depict the
conductive oligomer in the 3' position, although the 5' position is also possible. Furthermore, both
35 Structures 23 and 24 depict naturally occurring phosphodiester bonds, although as those in the art will
appreciate, non-standard analogs of phosphodiester bonds may also be used.

-38-

Structure 23

5

In Structure 23, if the terminal Y is present (i.e. m=1), then preferably Z is not present (i.e. t=0). If the
10 terminal Y is not present, then Z is preferably present.

15

20

35

Structure 24 depicts a preferred embodiment, wherein the terminal B-D bond is an amide bond, the
terminal Y is not present, and Z is a linker, as defined herein.

Structure 24

In a preferred embodiment, the conductive oligomer is covalently attached to the nucleic acid via a
transition metal ligand. In this embodiment, the conductive oligomer is covalently attached to a ligand
which provides one or more of the coordination atoms for a transition metal. In one embodiment, the
ligand to which the conductive oligomer is attached also has the nucleic acid attached, as is generally

25 depicted below in Structure 25. Alternatively, the conductive oligomer is attached to one ligand, and
the nucleic acid is attached to another iigand, as is generally depicted below in Structure 26. Thus, in
the presence of the transition metal, the conductive oligomer is covalently attached to the nucleic acid.
Both of these structures depict Structure 3 conductive oligomers, although other oligomers may be
utilized. Structures 25 and 26 depict two representative structures for nucleic acids; as will be

30 appreciated by those in the art, it is possible to connect other types of capture binding ligands, for
example proteinaceous binding ligands, in a similar manner:

Structure 25

-39-

Structure 26

nucleic acid

-(™K**-V l

5

In the structures depicted herein, M is a metal atom, with transition metals being preferred. Suitable
transition metals for use in the invention include, but are not limited to, cadmium (Cd), copper (Cu),
cobalt (Co), palladium (Pd), zinc (Zn), iron (Fe), ruthenium (Ru), rhodium (Rh), osmium (Os), rhenium
(Re), platinium (Pt), scandium (Sc), titanium (Ti), Vanadium (V), chromium (Cr), manganese (Mn),
10 nickel (Ni), Molybdenum (Mo), technetium (Tc), tungsten (W), and iridium (Ir). That is, the first series
of transition metals, the platinum metals (Ru, Rh, Pd, Os, Irand Pt), along with Fe, Re, W, Mo and Tc,
are preferred. Particularly preferred are ruthenium, rhenium, osmium, platinium, cobalt and iron.

L are the co-ligands, that provide the coordination atoms for the binding of the metal ion. As will be
15 appreciated by those in the art, the number and nature of the co-ligands will depend on the

coordination number of the metal ion. Mono-, di- or polydentate co-ligands may be used at any
position. Thus, for example, when the metal has a coordination number of six, the L from the terminus
of the conductive oligomer, the L contributed from the nucleic acid, and r, add up to six. Thus, when
the metal has a coordination number of six, r may range from zero (when all coordination atoms are
20 provided by the other two ligands) to four, when all the co-ligands are monodentate. Thus generally, r
will be from 0 to 8, depending on the coordination number of the metal ion and the choice of the other
ligands.

In one embodiment, the metal ion has a coordination number of six and both the ligand attached to the
25 conductive oligomer and the ligand attached to the nucleic acid are at least bidentate; that is, r is

preferably zero, one (i.e. the remaining co-ligand is bidentate) or two (two monodentate co-ligands are
used).

As will be appreciated in the art, the co-ligands can be the same or different. Suitable ligands fall into
30 two categories: ligands which use nitrogen, oxygen, sulfur, carbon or phosphorus atoms (depending
on the metal ion) as the coordination atoms (generally referred to in the literature as sigma (o) donors)
and organometallic ligands such as metallocene ligands (generally referred to in the literature as pi (n)
donors, and depicted herein as L m ). Suitable nitrogen donating ligands are well known in the art and
include, but are not limited to, NH 2 ; NHR; NRR'; pyridine; pyrazine; isonicotinamide; imidazole;
35 bipyridine and substituted derivatives of bipyridine; terpyridine and substituted derivatives;

phenanthrolines, particularly 1,10-phenanthroline (abbreviated phen) and substituted derivatives of
phenanthrolines such as 4,7-dimethylphenanthroline and dipyridol[3,2-a:2',3'-c]phenazine (abbreviated

-40 -

dppz); dipyridophenazine; 1,4,5,8,9,12-hexaazatriphenylene (abbreviated hat); 9,10-
phenanthrenequinone diimine (abbreviated phi); 1,4,5,8-tetraazaphenanthrene (abbreviated tap);
1,4,8,1 1-tetra-azacyclotetradecane (abbreviated cyclam), EDTA, EGTA and isocyanide. Substituted
derivatives, including fused derivatives, may also be used. In some embodiments, porphyrins and
5 substituted derivatives of the porphyrin family may be used. See for example, Comprehensive

Coordination Chemistry, Ed. Wilkinson et al., Pergammon Press, 1987, Chapters 13.2 (pp73-98), 21.1
(pp. 813-898) and 21.3 (pp 915-957), all of which are hereby expressly incorporated by reference.

Suitable sigma donating ligands using carbon, oxygen, sulfur and phosphorus are known in the art.
10 For example, suitable sigma carbon donors are found in Cotton and Wilkenson, Advanced Organic
Chemistry, 5th Edition, John Wiley & Sons, 1988, hereby incorporated by reference; see page 38, for
example. Similarly, suitable oxygen ligands include crown ethers, water and others known in the art.
Phosphines and substituted phosphines are also suitable; see page 38 of Cotton and Wilkenson.

15 The oxygen, sulfur, phosphorus and nitrogen-donating ligands are attached in such a manner as to
allow the heteroatoms to serve as coordination atoms.

In a preferred embodiment, organometallic ligands are used. In addition to purely organic compounds
for use as redox moieties, and various transition metal coordination complexes with 5-bonded organic

20 ligand with donor atoms as heterocyclic or exocyclic substituents, there is available a wide variety of
transition metal organometallic compounds with rr-bonded organic ligands (see Advanced Inorganic
Chemistry, 5th Ed., Cotton & Wilkinson, John Wiley & Sons, 1988, chapter 26; Organometallics, A
Concise Introduction, Elschenbroich et al., 2nd Ed., 1992, VCH; and Comprehensive Organometallic
Chemistry II, A Review of the Literature 1982-1994, Abel et al. Ed., Vol. 7, chapters 7, 8, 10 & 1 1,

25 Pergamon Press, hereby expressly incorporated by reference). Such organometallic ligands include
cyclic aromatic compounds such as the cyclopentadienide ion [C 5 H 5 (-1)] and various ring substituted
and ring fused derivatives, such as the indenylide (-1) ion, that yield a class of bis(cyclopentadieyl)
metal compounds, (i.e. the metallocenes); see for example Robins et al., J. Am. Chem. Soc.
104:1882-1893 (1982); and Gassman et al., J. Am. Chem. Soc. 108:4228-4229(1986),

30 incorporated by reference. Of these, ferrocene [(C 5 H 5 ) 2 Fe] and its derivatives are prototypical

examples which have been used in a wide variety of chemical (Connelly et al., Chem. Rev. 96:877-
910 (1996), incorporated by reference) and electrochemical (Geigeretal., Advances in
Organometallic Chemistry 23:1-93; and Geiger et al., Advances in Organometallic Chemistry 24:87,
incorporated by reference) electron transfer or "redox" reactions. Metallocene derivatives of a variety

35 of the first, second and third row transition metals are potential candidates as redox moieties that are
covalently attached to either the ribose ring or the nucleoside base of nucleic acid. Other potentially
suitable organometallic ligands include cyclic arenes such as benzene, to yield bis(arene)metal

-41 -

compounds and their ring substituted and ring fused derivatives, of which bis(benzene)chromium is a
prototypical example, Other acyclic n-bonded ligands such as the allyl(-1) ion, or butadiene yield
potentially suitable organometallic compounds, and all such ligands, in conjuction with other n-bonded
and 5-bonded ligands constitute the general class of organometallic compounds in which there is a
5 metal to carbon bond. Electrochemical studies of various dimers and oligomers of such compounds
with bridging organic ligands, and additional non-bridging ligands, as well as with and without metal-
metal bonds are potential candidate redox moieties in nucleic acid analysis.

When one or more of the co-ligands is an organometallic ligand, the ligand is generally attached via
10 one of the carbon atoms of the organometallic ligand, although attachment may be via other atoms for
heterocyclic ligands. Preferred organometallic ligands include metallocene ligands, including
substituted derivatives and the metalloceneophanes (see page 1174 of Cotton and Wilkenson, supra).
For example, derivatives of metallocene ligands such as methylcyclopentadienyl, with multiple methyl
groups being preferred, such as pentamethylcyclopentadienyl, can be used to increase the stability of
15 the metallocene. In a preferred embodiment, only one of the two metallocene ligands of a metallocene
are derivatized.

As described herein, any combination of ligands may be used. Preferred combinations include: a) all
ligands are nitrogen donating ligands; b) all ligands are organometallic ligands; and c) the ligand at the

20 terminus of the conductive oligomer is a metallocene ligand and the ligand provided by the nucleic acid
is a nitrogen donating ligand, with the other ligands, if needed, are either nitrogen donating ligands or
metallocene ligands, or a mixture. These combinations are depicted in representative structures using
the conductive oligomer of Structure 3 are depicted in Structures 27 (using phenanthroline and amino
as representative ligands), 28 (using ferrocene as the metal-ligand combination) and 29 (using

25 cyclopentadienyl and amino as representative ligands).

Structure 27

30

35

-42-

Structure 29

10

15

In a preferred embodiment, the ligands used in the invention show altered fluoroscent properties
depending on the redox state of the chelated metal ion. As described below, this thus serves as an
additional mode of detection of electron transfer between the ETM and the electrode.

In a preferred embodiment, as is described more fully below, the ligand attached to the nucleic acid is
an amino group attached to the 2' or 3' position of a ribose of the ribose-phosphate backbone. This
ligand may contain a multiplicity of amino groups so as to form a polydentate ligand which binds the
metal ion. Other preferred ligands include cyclopentadiene and phenanthroline.

The use of metal ions to connect the nucleic acids can serve as an internal control or calibration of the
system, to evaluate the number of available nucleic acids on the surface. However, as will be
appreciated by those in the art, if metal ions are used to connect the nucleic acids to the conductive
oligomers, it is generally desirable to have this metal ion complex have a different redox potential than

20 that of the ETMs used in the rest of the system, as described below. This is generally true so as to be
able to distinguish the presence of the capture probe from the presence of the target sequence. This
may be useful for identification, calibration and/or quantification. Thus, the amount of capture probe
on an electrode may be compared to the amount of hybridized double stranded nucleic acid to quantify
the amount of target sequence in a sample. This is quite significant to serve as an internal control of

25 the sensor or system. This allows a measurement either prior to the addition of target or after, on the
same molecules that will be used for detection, rather than rely on a similar but different control
system. Thus, the actual molecules that will be used for the detection can be quantified prior to any
experiment. This is a significant advantage over prior methods.

30 In a preferred embodiment, the capture probe nucleic acids are covalently attached to the electrode

via an insulator. The attachment of nucleic acids to insulators such as alkyl groups is well known, and
can be done to the base or the backbone, including the ribose or phosphate for backbones containing
these moieties, or to alternate backbones for nucleic acid analogs.

35 In a preferred embodiment, the capture binding ligands are covalently attached to the electrode via an
insulator. The attachment of a variety of binding ligands such as proteins and nucleic acids to
insulators such as alkyl groups is well known, and can be done to the nucleic acid bases or the

-43-

backbone, including the ribose or phosphate for backbones containing these moieties, or to alternate
backbones for nucleic acid analogs, or to the side chains or backbone of the amino acids.

In a preferred embodiment, there may be one or more different capture binding ligand species
5 (sometimes referred to herein as "anchor ligands", "anchor probes" or "capture probes" with the

phrase "probe" generally referring to nucleic acid species) on the surface, as is generally depicted in
the Figures. In some embodiments, there may be one type of capture binding ligand, or one type of
capture binding ligand extender, as is more fully described below. Alternatively, different capture
binding ligands, or one capture binding ligand with a multiplicity of different capture extender binding
10 ligands can be used. Similarly, when nucleic acid systems are used, it may be desirable to use

auxiliary capture probes that comprise relatively short probe sequences, that can be used to "tack
down" components of the system, for example the recruitment linkers, to increase the concentration of
ETMs at the surface.

15 Thus the present invention provides electrodes comprising monolayers comprising conductive
oligomers and capture binding ligands, useful in target analyte detection systems.

In a preferred embodiment, the compositions further comprise a solution binding ligand. Solution
binding ligands are similar to capture binding ligands, in that they bind to target analytes. The solution
20 binding ligand may be the same or different from the capture binding ligand. Generally, the solution
binding ligands are not directly attached to the surface, although as depicted in Figure 5A they may
be. The solution binding ligand either directly comprises a recruitment linker that comprises at least
one ETM, or the recruitment linker is part of a label probe that will bind to the solution binding ligand.

25 Thus, "recruitment linkers" or "signal carriers" with covalently attached ETMs are provided. The terms
"electron donor moiety", "electron acceptor moiety", and "ETMs" (ETMs) or grammatical equivalents
herein refers to molecules capable of electron transfer under certain conditions. It is to be understood
that electron donor and acceptor capabilities are relative; that is, a molecule which can lose an
electron under certain experimental conditions will be able to accept an electron under different

30 experimental conditions. It is to be understood that the number of possible electron donor moieties
and electron acceptor moieties is very large, and that one skilled in the art of electron transfer
compounds will be able to utilize a number of compounds in the present invention. Preferred ETMs
include, but are not limited to, transition metal complexes, organic ETMs, and electrodes.

35 In a preferred embodiment, the ETMs are transition metal complexes. Transition metals are those
whose atoms have a partial or complete d shell of electrons. Suitable transition metals for use in the
invention are listed above.

-44 -

The transition metals are complexed with a variety of ligands, L, defined above, to form suitable
transition metal complexes, as is well known in the art.

In addition to transition metal complexes, other organic electron donors and acceptors may be
5 covalently attached to the nucleic acid for use in the invention. These organic molecules include, but
are not limited to, riboflavin, xanthene dyes, aztne dyes, acridine orange, A/,/V-dimethyl-2,7-
diazapyrenium dichloride (DAP 2+ ), methylviologen, ethidium bromide, quinones such as N,N'-
dimethylanthra(2,1 ,9-def.6,5,10-d'e'f)diisoquinoline dichloride (ADIQ 2+ ); porphyrins ([meso-tetrakis(N-
methyl-x-pyridinium)porphyrin tetrachloride], varlamine blue B hydrochloride, Bindschedler's green;

10 2,6-dichloroindophenol, 2,6-dibromophenolindophenol; Brilliant crest blue (3-amino-9-dimethyl-amino-
10-methylphenoxyazrne chloride), methylene blue; Nile blue A {aminoaphthodiethylaminophenoxazine
sulfate), indigo-5,5',7,7'-tetrasulfonic acid, indigo-5,5',7-trisulfonic acid; phenosafranine, indigo-5-
monosulfonic acid; safranine T; bis(dimethylglyoximato)-iron{ll) chloride; induline scarlet, neutral red,
anthracene, coronene, pyrene, 9-phenylanthracene, rubrene, binaphthyl, DPA, phenothiazene,

15 fluoranthene, phenanthrene, chrysene, 1,8-diphenyl-1,3,5,7-octatetracene, naphthalene,

acenaphthalene, perylene, TMPD and analogs and subsitituted derivatives of these compounds.

In one embodiment, the electron donors and acceptors are redox proteins as are known in the art.
However, redox proteins in many embodiments are not preferred.

20

The choice of the specific ETMs will be influenced by the type of electron transfer detection used, as is
generally outlined below. Preferred ETMs are metallocenes, with ferrocene being particularly
preferred.

25 In a preferred embodiment, a plurality of ETMs are used. As is shown in the examples, the use of
multiple ETMs provides signal amplification and thus allows more sensitive detection limits.
Accordingly, pluralities of ETMs are preferred, with at least about 2 ETMs per recruitment linker being
preferred, and at least about 10 being particularly preferred, and at least about 20 to 50 being
especially preferred. In some instances, very large numbers of ETMs (100 to 1000) can be used.

30

As will be appreciated by those in the art, the portion of the label probe (or target, in some
embodiments) that comprises the ETMs (termed herein a "recruitment linker" or "signal carrier") can
be nucleic acid, or it can be a non-nucleic acid linker that links the solution binding ligand to the ETMs.
Thus, as will be appreciated by those in the art, there are a variety of configurations that can be used.
35 In a preferred embodiment, the recruitment linker is nucleic acid (including analogs), and attachment
of the ETMs can be via (1) a base; (2) the backbone, including the ribose, the phosphate, or
comparable structures in nucleic acid analogs; (3) nucleoside replacement, described below; or (4)

-45-

metallocene polymers, as described below. In a preferred embodiment, the recruitment linker is non-
nucleic acid, and can be either a metallocene polymer or an alkyl-type polymer (including heteroalkyl,
as is more fully described below) containing ETM substitution groups.

5 In a preferred embodiment, the recruitment linker is a nucleic acid, and comprises covalently attached
ETMs. The ETMs may be attached to nucleosides within the nucleic acid in a variety of positions.
Preferred embodiments include, but are not limited to, (1) attachment to the base of the nucleoside, (2)
attachment of the ETM as a base replacement, (3) attachment to the backbone of the nucleic acid,
including either to a ribose of the ribose-phosphate backbone or to a phosphate moiety, or to
10 analogous structures in nucleic acid analogs, and (4) attachment via metallocene polymers, with the
latter being preferred.

In addition, as is described below, when the recruitment linker is nucleic acid, it may be desirable to
use secondary label probes, that have a first portion that will hybridize to a portion of the primary label
15 probes and a second portion comprising a recruitment linker as is defined herein. This is generally
depicted in Figure 7Q and 7R; this is similar to the use of an amplifier probe, except that both the
primary and the secondary label probes comprise ETMs.

In a preferred embodiment, the ETM is attached to the base of a nucleoside as is generally outlined
20 above for attachment of the conductive oligomer. Attachment can be to an internal nucleoside or a
terminal nucleoside.

The covalent attachment to the base will depend in part on the ETM chosen, but in general is similar to
the attachment of conductive oligomers to bases, as outlined above. Attachment may generally be
25 done to any position of the base. In a preferred embodiment, the ETM is a transition metal complex,
and thus attachment of a suitable metal ligand to the base leads to the covalent attachment of the
ETM. Alternatively, similar types of linkages may be used for the attachment of organic ETMs, as will
be appreciated by those in the art.

30 In one embodiment, the C4 attached amino group of cytosine, the C6 attached amino group of
adenine, or the C2 attached amino group of guanine may be used as a transition metal ligand.

Ligands containing aromatic groups can be attached via acetylene linkages as is known in the art (see
Comprehensive Organic Synthesis, Trost eta!., Ed., Pergamon Press, Chapter 2.4: Coupling
35 Reactions Between sp 2 and sp Carbon Centers, Sonogashira, pp521-549, and pp950-953, hereby
incorporated by reference). Structure 30 depicts a representative structure in the presence of the

-46-

metal ion and any other necessary ligands; Structure 30 depicts uridine, although as for all the
structures herein, any other base may also be used.

Structure 30

10

15

L a is a ligand, which may include nitrogen, oxygen, sulfur or phosphorus donating ligands or
organometallic ligands such as metailocene ligands. Suitable L a ligands include, but not limited to,
phenanthroline, imidazole, bpy and terpy. L r and M are as defined above. Again, it will be appreciated
by those in the art, a linker ("Z") may be included between the nucleoside and the ETM.

Similarly, as for the conductive oligomers, the linkage may be done using a linker, which may utilize an
amide linkage (see generally Telser et al., J. Am. Chem. Soc. 111:7221-7226 (1989); Telser et al., J.
Am. Chem. Soc. 111:7226-7232 (1989), both of which are expressly incorporated by reference).
20 These structures are generally depicted below in Structure 31 , which again uses uridine as the base,
although as above, the other bases may also be used:

Structure 31

25

30 In this embodiment, L is a ligand as defined above, with L r and M as defined above as well.
Preferably, L is amino, phen, byp and terpy.

In a preferred embodiment, the ETM attached to a nucleoside is a metailocene; i.e. the L and L r of
Structure 31 are both metailocene ligands, L m , as described above. Structure 32 depicts a preferred
35 embodiment wherein the metailocene is ferrocene, and the base is uridine, although other bases may
be used:

-47-

Structure 32

o

5

Preliminary data suggest that Structure 32 may cyclize, with the second acetylene carbon atom
10 attacking the carbonyl oxygen, forming a furan-like structure. Preferred metallocenes include
ferrocene, cobaltocene and osmiumocene.

In a preferred embodiment, the ETM is attached to a ribose at any position of the ribose-phosphate
backbone of the nucleic acid, i.e. either the 5' or 3' terminus or any internal nucleoside. Ribose in this

15 case can include ribose analogs. As is known in the art, nucleosides that are modified at either the 2'
or 3' position of the ribose can be made, with nitrogen, oxygen, sulfur and phosphorus-containing
modifications possible. Ami no-modified and oxygen-modified ribose is preferred. See generally PCT
publication WO 95/15971, incorporated herein by reference. These modification groups may be used
as a transition metal ligand, or as a chemically functional moiety for attachment of other transition

20 metal ligands and organometallic ligands, or organic electron donor moieties as will be appreciated by
those in the art. In this embodiment, a linker such as depicted herein for "Z" may be used as well, or a
conductive oligomer between the ribose and the ETM. Preferred embodiments utilize attachment at
the 2' or 3' position of the ribose, with the 2' position being preferred. Thus for example, the
conductive oligomers depicted in Structure 13, 14 and 15 may be replaced by ETMs; alternatively, the

25 ETMs may be added to the free terminus of the conductive oligomer.

In a preferred embodiment, a metallocene serves as the ETM, and is attached via an amide bond as
depicted below in Structure 33. The examples outline the synthesis of a preferred compound when
the metallocene is ferrocene.

30

Structure 33

35

%

-48-

In a preferred embodiment, amine linkages are used, as is generally depicted in Structure 34.

Structure 34

5

ETM

Z is a linker, as defined herein, with 1-16 atoms being preferred, and 2-4 atoms being particularly
10 preferred, and t is either one or zero.

In a preferred embodiment, oxo linkages are used, as is generally depicted in Structure 35.

Structure 35

15

20 In Structure 35, Z is a linker, as defined herein, and t is either one or zero. Preferred Z linkers include
alkyl groups including heteroalkyl groups such as (CH 2 )n and (CH 2 CH 2 0)n, with n from 1 to 10 being
preferred, and n = 1 to 4 being especially preferred, and n=4 being particularly preferred.

Linkages utilizing other heteroatoms are also possible.

25

In a preferred embodiment, an ETM is attached to a phosphate at any position of the ribose-phosphate
backbone of the nucleic acid. This may be done in a variety of ways. In one embodiment,
phosphodiester bond analogs such as phosphoramide or phosphoramidite linkages may be
incorporated into a nucleic acid, where the heteroatom (i.e. nitrogen) serves as a transition metal
30 ligand (see PCT publication WO 95/15971, incorporated by reference). Alternatively, the conductive
oligomers depicted in Structures 23 and 24 may be replaced by ETMs. In a preferred embodiment,
the composition has the structure shown in Structure 36.

35

-49-

Structure 36

5

I

o

In Structure 361, the ETM is attached via a phosphate linkage, generally through the use of a linker, Z.
10 Preferred Z linkers include alkyl groups, including heteroalkyl groups such as (CH 2 ) n , (CH 2 CH 2 0) n , with
n from 1 to 10 being preferred, and n = 1 to 4 being especially preferred, and n=4 being particularly
preferred.

When the ETM is attached to the base or the backbone of the nucleoside, it is possible to attach the
15 ETMs via "dendrimer" structures, as is more fully outlined below. Alkyl-based linkers can be used to
create multiple branching structures comprising one or more ETMs at the terminus of each branch.
Generally, this is done by creating branch points containing multiple hydroxy groups, which optionally
can then be used to add additional branch points. The terminal hydroxy groups can then be used in
phosphoramidite reactions to add ETMs, as is generally done below for the nucleoside replacement
20 and metallocene polymer reactions.

In a preferred embodiment, an ETM such as a metallocene is used as a "nucleoside replacement",
serving as an ETM. For example, the distance between the two cyclopentadiene rings of ferrocene is
similar to the orthongonal distance between two bases in a double stranded nucleic acid. Other

25 metallocenes in addition to ferrocene may be used, for example, air stable metallocenes such as those
containing cobalt or ruthenium. Thus, metallocene moieties may be incorporated into the backbone of
a nucleic acid, as is generally depicted in Structure 37 (nucleic acid with a ribose-phosphate
backbone) and Structure 38 (peptide nucleic acid backbone). Structures 37 and 38 depict ferrocene,
although as will be appreciated by those in the art, other metallocenes may be used as well. In

30 general, air stable metallocenes are preferred, including metallocenes utilizing ruthenium and cobalt as
the metal.

35

-50-

Structure 37

BASE

O

0 P^'

Fe

o-

O

\

Chfe BASE

In Structure 37, Z is a linker as defined above, with generally short, alkyl groups, including
heteroatoms such as oxygen being preferred. Generally, what is important is the length of the linker,
such that minimal perturbations of a double stranded nucleic acid is effected, as is more fully
described below. Thus, methylene, ethylene, ethylene glycols, propylene and butylene are all
preferred, with ethylene and ethylene glycol being particularly preferred. In addition, each Z linker may
be the same or different. Structure 37 depicts a ribose-phosphate backbone, although as will be
appreciated by those in the art, nucleic acid analogs may also be used, including ribose analogs and
phosphate bond analogs.

Structure 38

HM

-51 -

In Structure 38, preferred Z groups are as listed above, and again, each Z linker can be the same or
different. As above, other nucleic acid analogs may be used as well.

In addition, although the structures and discussion above depicts metallocenes, and particularly
5 ferrocene, this same general idea can be used to add ETMs in addition to metallocenes, as nucleoside
replacements or in polymer embodiments, described below. Thus, for example, when the ETM is a
transition metal complex other than a metallocene, comprising one, two or three (or more) ligands, the
ligands can be functionalized as depicted for the ferrocene to allow the addition of phosphoramidite
groups. Particularly preferred in this embodiment are complexes comprising at least two ring (for
10 example, aryl and substituted aryl) ligands, where each of the ligands comprises functional groups for
attachment via phosphoramidite chemistry. As will be appreciated by those in the art, this type of
reaction, creating polymers of ETMs either as a portion of the backbone of the nucleic acid or as "side
groups" of the nucleic acids, to allow amplification of the signals generated herein, can be done with
virtually any ETM that can be functionalized to contain the correct chemical groups.

15

Thus, by inserting a metallocene such as ferrocene (or other ETM) into the backbone of a nucleic acid,
nucleic acid analogs are made; that is, the invention provides nucleic acids having a backbone
comprising at least one metallocene. This is distinguished from nucleic acids having metallocenes
attached to the backbone, i.e. via a ribose, a phosphate, etc. That is, two nucleic acids each made up
20 of a traditional nucleic acid or analog (nucleic acids in this case including a single nucleoside), may be
covalently attached to each other via a metallocene. Viewed differently, a metallocene derivative or
substituted metallocene is provided, wherein each of the two aromatic rings of the metallocene has a
nucleic acid substitutent group.

25 In addition, as is more fully outlined below, it is possible to incorporate more than one metallocene into
the backbone, either with nucleotides in between and/or with adjacent metallocenes. When adjacent
metallocenes are added to the backbone, this is similar to the process described below as
"metallocene polymers"; that is, there are areas of metallocene polymers within the backbone.

30 In addition to the nucleic acid substitutent groups, it is also desirable in some instances to add

additional substituent groups to one or both of the aromatic rings of the metallocene (or ETM). For
example, as these nucleoside replacements are generally part of probe sequences to be hybridized
with a substantially complementary nucleic acid, for example a target sequence or another probe
sequence, it is possible to add substitutent groups to the metallocene rings to facilitate hydrogen

35 bonding to the base or bases on the opposite strand. These may be added to any position on the
metallocene rings. Suitable substitutent groups include, but are not limited to, amide groups, amine

-52-

groups, carboxylic acids, and alcohols, including substituted alcohols. In addition, these substitutent
groups can be attached via linkers as well, although in general this is not preferred.

10

20

25

30

In addition, substituent groups on an ETM, particularly metallocenes such as ferrocene, may be added
to alter the redox properties of the ETM. Thus, for example, in some embodiments, as is more fully
described below, it may be desirable to have different ETMs attached in different ways (i.e. base or
ribose attachment), on different probes, or for different purposes (for example, calibration or as an
internal standard). Thus, the addition of substituent groups on the metallocene may allow two different
ETMs to be distinguished.

In order to generate these metallocene-backbone nucleic acid analogs, the intermediate components
are also provided. Thus, in a preferred embodiment, the invention provides phosphoramidite
metallocenes, as generally depicted in Structure 39:

Structure 39

15 pg — o

Z AROMATIC RIN

M

-AROMATIC RIN

I H Xhk
NCKCHjC P / ^

^CH^ ^CHa
H 3 C CH3

In Structure 39, PG is a protecting group, generally suitable for use in nucleic acid synthesis, with
DMT, MMT and TMT all being preferred. The aromatic rings can either be the rings of the
metallocene, or aromatic rings of ligands for transition metal complexes or other organic ETMs. The
aromatic rings may be the same or different, and may be substituted as discussed herein.

Structure 40 depicts the ferrocene derivative:

35

-53-

Structure 40

10

H ^CH 3

NCH 2 CH 2 C P N-^/ 3

| un

H3C CH3

15

These phosphoramidite analogs can be added to standard oligonucleotide syntheses as is known in
the art.

Structure 41 depicts the ferrocene peptide nucleic acid (PNA) monomer, that can be added to PNA
synthesis (or regular protein synthesis) as is known in the art and as illustrated in PCT/US99/10104
and PCT/US00/20476, incorporated herein by reference:

20

25

Structure 41

PG NH

o^=c.

/
\

OH

30

In Structure 41, the PG protecting group is suitable for use in peptide nucleic acid synthesis, with
MMT, boc and Fmoc being preferred.

These same intermediate compounds can be used to form ETM or metallocene polymers, which are
added to the nucleic acids, rather than as backbone replacements, as is more fully described below.

In a preferred embodiment, the ETMs are attached as polymers, for example as metallocene
35 polymers, in a "branched" configuration similar to the "branched DNA" embodiments herein and as

outlined in U.S. Patent No. 5,124,246, using modified functionalized nucleotides. The general idea is
as follows. A modified phosphoramidite nucleotide is generated that can ultimately contain a free

- 54 -

hydroxy group that can be used in the attachment of phosphoramidite ETMs such as metallocenes.
This free hydroxy group could be on the base or the backbone, such as the ribose or the phosphate
(although as will be appreciated by those in the art, nucleic acid analogs containing other structures
can also be used). The modified nucleotide is incorporated into a nucleic acid, and any hydroxy
5 protecting groups are removed, thus leaving the free hydroxyl. Upon the addition of a

phosphoramidite ETM such as a metallocene, as described above in structures 39 and 40, ETMs,
such as metallocene ETMs, are added. Additional phosphoramidite ETMs such as metallocenes can
be added, to form "ETM polymers", including "metallocene polymers" as depicted in PCT/US99/10104.
In addition, in some embodiments, it is desirable to increase the solubility of the polymers by adding a
10 "capping" group to the terminal ETM in the polymer. Other suitable solubility enhancing "capping"

groups will be appreciated by those in the art. It should be noted that these solubility enhancing groups
can be added to the polymers in other places, including to the ligand rings, for example on the
metallocenes as discussed herein.

15 Briefly, the 2' position of a ribose of a phosphoramidite nucleotide is first functionalized to contain a

protected hydroxy group, in this case via an oxo-linkage, although any number of linkers can be used,
as is generally described herein for Z linkers. The protected modified nucleotide is then incorporated
via standard phosphoramidite chemistry into a growing nucleic acid. The protecting group is removed,
and the free hydroxy group is used, again using standard phosphoramidite chemistry to add a

20 phosphoramidite metallocene such as ferrocene. A similar reaction is possible for nucleic acid

analogs. For example, using peptide nucleic acids and the metallocene monomer shown in Structure
41, peptide nucleic acid structures containing metallocene polymers could be generated.

Thus, the present invention provides recruitment linkers of nucleic acids comprising "branches" of
25 metallocene polymers. Preferred embodiments also utilize metallocene polymers from one to about
50 metallocenes in length, with from about 5 to about 20 being preferred and from about 5 to about 10
being especially preferred.

In addition, when the recruitment linker is nucleic acid, any combination of ETM attachments may be
30 done.

In a preferred embodiment, the recruitment linker is not nucleic acid, and instead may be any sort of
linker or polymer. As will be appreciated by those in the art, generally any linker or polymer that can be
modified to contain ETMs can be used. In general, the polymers or linkers should be reasonably
35 soluble and contain suitable functional groups for the addition of ETMs.

-55-

As used herein, a "recruitment polymer" comprises at least two or three subunits, which are covalently
attached. At least some portion of the monomeric subunits contain functional groups for the covalent
attachment of ETMs. In some embodiments coupling moieties are used to covalently link the subunits
with the ETMs. Preferred functional groups for attachment are amino groups, carboxy groups, oxo
5 groups and thiol groups, with amino groups being particularly preferred. As will be appreciated by
those in the art, a wide variety of recruitment polymers are possible.

Suitable linkers include, but are not limited to, alkyl linkers (including heteroalkyl {including
(poly)ethylene glycol-type structures), substituted alkyl, aryalkyl linkers, etc. As above for the
10 polymers, the linkers will comprise one or more functional groups for the attachment of ETMs, which
will be done as will be appreciated by those in the art, for example through the use homo-or hetero-
bifunctional linkers as are well known (see 1994 Pierce Chemical Company catalog, technical section
on cross-linkers, pages 155-200, incorporated herein by reference).

15 Suitable recruitment polymers include, but are not limited to, functionalized styrenes, such as amino
styrene, functionalized dextrans, and polyamino acids. Preferred polymers are polyamino acids (both
poly-D-amino acids and poly-L-amino acids), such as polylysine, and polymers containing lysine and
other amino acids being particularly preferred. Other suitable polyamino acids are polyglutamic acid,
polyaspartic acid, co-polymers of lysine and glutamic or aspartic acid, co-polymers of lysine with

20 alanine, tyrosine, phenylalanine, serine, tryptophan, and/or proline.

In a preferred embodiment, the recruitment linker comprises a metallocene polymer, as is described
above.

25 The attachment of the recruitment linkers to either the solution binding ligand or the first portion of the
label probe will depend on the composition of the recruitment linker and of the label and/or binding
ligand, as will be appreciated by those in the art. When either the label probe or the binding ligand is
nucleic acid, nucleic acid recruitment linkers are generally formed during the synthesis of the first
species, with incorporation of nucleosides containing ETMs as required. Alternatively, the first portion

30 of the label probe or the binding ligand and the recruitment linker may be made separately, and then
attached. When they are both nucleic acid, there may be an overlapping section of complementarity,
forming a section of double stranded nucleic acid that can then be chemically crosslinked, for example
by using psoralen as is known in the art.

35 When non-nucleic acid recruitment linkers are used, attachment of the linker/polymer of the
recruitment linker will be done generally using standard chemical techniques, such as will be

-56-

appreciated by those in the art. For example, when alkyl-based linkers are used, attachment can be
similar to the attachment of insulators to nucleic acids.

In addition, it is possible to have recruitment linkers that are mixtures of nucleic acids and non-nucleic
5 acids, either in a linear form (i.e. nucleic acid segments linked together with alkyl linkers) or in

branched forms {nucleic acids with alkyl "branches" that may contain ETMs and may be additionally
branched).

In a preferred embodiment, it is the target sequence itself that carries the ETMs, rather than the
10 recruitment linker of a label probe. For example, as is more fully described below, it is possible to

enzymatically add triphosphate nucleotides comprising the ETMs of the invention to a growing nucleic
acid, for example during a polymerase chain reaction (PCR). As will be recognized by those in the art,
while several enzymes have been shown to generally tolerate modified nucleotides, some of the
modified nucleotides of the invention, for example the "nucleoside replacement" embodiments and
15 putatively some of the phosphate attachments, may or may not be recognized by the enzymes to

allow incorporation into a growing nucleic acid. Therefore, preferred attachments in this embodiment
are to the base or ribose of the nucleotide.

Thus, for example, PCR amplification of a target sequence, as is well known in the art, will result in
20 target sequences comprising ETMs, generally randomly incorporated into the sequence.

Alternatively, as outlined more fully below, it is possible to enzymatically add nucleotides comprising
ETMs to the terminus of a nucleic acid, for example a target nucleic acid. In this embodiment, an
effective "recruitment linker" is added to the terminus of the target sequence, that can then be used for
25 detection. Thus the invention provides compositions utilizing electrodes comprising monolayers of
conductive oligomers and capture probes, and target sequences that comprises a first portion that is
capable of hybridizing to a component of an assay complex, and a second portion that does not
hybridize to a component of an assay complex and comprises at least one covalently attached
electron transfer moiety. Similarly, methods utilizing these compositions are also provided.

30

It is also possible to have ETMs connected to probe sequences, i.e. sequences designed to hybridize
to complementary sequences. Thus, ETMs may be added to non-recruitment linkers as well. For
example, there may be ETMs added to sections of label probes that do hybridize to components of the
assay complex, for example the first portion, or to the target sequence as outlined above and depicted
35 in Figure 7R. These ETMs may be used for electron transfer detection in some embodiments, or they
may not, depending on the location and system. For example, in some embodiments, when for
example the target sequence containing randomly incorporated ETMs is hybridized directly to the

-57-

capture probe, as is depicted in Figure 7A and 7B, there may be ETMs in the portion hybridizing to the
capture probe. If the capture probe is attached to the electrode using a conductive oligomer, these
ETMs can be used to detect electron transfer as has been previously described. Alternatively, these
ETMs may not be specifically detected.

5

Similarly, in some embodiments, when the recruitment linker is nucleic acid, it may be desirable in
some instances to have some or all of the recruitment linker be double stranded. In one embodiment,
there may be a second recruitment linker, substantially complementary to the first recruitment linker,
that can hybridize to the first recruitment linker. In a preferred embodiment, the first recruitment linker

10 comprises the covalently attached ETMs. In an alternative embodiment, the second recruitment linker
contains the ETMs, and the first recruitment linker does not, and the ETMs are recruited to the surface
by hybridization of the second recruitment linker to the first. In yet another embodiment, both the first
and second recruitment linkers comprise ETMs. It should be noted, as discussed above, that nucleic
acids comprising a large number of ETMs may not hybridize as well, i.e. the T m may be decreased,

15 depending on the site of attachment and the characteristics of the ETM. Thus, in general, when

multiple ETMs are used on hybridizing strands, generally there are less than about 5, with less than
about 3 being preferred, or alternatively the ETMs should be spaced sufficiently far apart that the
intervening nucleotides can sufficiently hybridize to allow good kinetics.

20 In one embodiment, when nucleic acid targets and/or binding ligands and/or recruitment linkers are
used, non-covalently attached ETMs may be used. In one embodiment, the ETM is a hybridization
indicator. Hybridization indicators serve as an ETM that will preferentially associate with double
stranded nucleic acid is added, usually reversibly, similar to the method of Millan et al., Anal. Chem.
65:2317-2323 (1993); Millan et al., Anal. Chem. 662943-2948 (1994), both of which are hereby

25 expressly incorporated by reference. In this embodiment, increases in the local concentration of

ETMs, due to the association of the ETM hybridization indicator with double stranded nucleic acid at
the surface, can be monitored using the monolayers comprising the conductive oligomers.
Hybridization indicators include intercalators and minor and/or major groove binding moieties. In a
preferred embodiment, intercalators may be used; since intercalation generally only occurs in the

30 presence of double stranded nucleic acid, only in the presence of double stranded nucleic acid will the
ETMs concentrate. Intercalating transition metal complex ETMs are known in the art. Similarly, major
or minor groove binding moieties, such as methylene blue, may also be used in this embodiment.

Similarly, the systems of the invention may utilize non-covalently attached ETMs, as is generally
35 described in Napier etal., Bioconj. Chem. 8:906 (1997), hereby expressly incorporated by reference.
In this embodiment, changes in the redox state of certain molecules as a result of the presence of

-58-

DNA (i.e. guanine oxidation by ruthenium complexes) can be detected using the SAMs comprising
conductive oligomers as weil.

Thus, the present invention provides electrodes comprising monolayers comprising conductive
5 oligomers, generally including capture binding ligands, and either binding ligands or label probes that
will bind to the binding ligands comprising recruitment linkers containing ETMs.

In a preferred embodiment, the compositions of the invention are used to detect target analytes in a
sample. In a preferred embodiment, the target analyte is a nucleic acid, and thus detection of target

10 sequences is done. The term "target sequence" or grammatical equivalents herein means a nucleic
acid sequence on a single strand of nucleic acid. The target sequence may be a portion of a gene, a
regulatory sequence, genomic DNA, cDNA, RNA including mRNA and rRNA, or others. It may be any
length, with the understanding that longer sequences are more specific. As will be appreciated by
those in the art, the complementary target sequence may take many forms. For example, it may be

15 contained within a larger nucleic acid sequence, i.e. all or part of a gene or mRNA, a restriction

fragment of a plasmid or genomic DNA, among others. As is outlined more fully below, probes are
made to hybridize to target sequences to determine the presence or absence of the target sequence
in a sample. Generally speaking, this term will be understood by those skilled in the art. The target
sequence may also be comprised of different target domains; for example, a first target domain of the

20 sample target sequence may hybridize to a capture probe or a portion of capture extender probe, a
second target domain may hybridize to a portion of an amplifier probe, a label probe, or a different
capture or capture extender probe, etc. The target domains may be adjacent or separated. The terms
"first" and "second" are not meant to confer an orientation of the sequences with respect to the 5'-3'
orientation of the target sequence. For example, assuming a 5'-3' orientation of the complementary

25 target sequence, the first target domain may be located either 5' to the second domain, or 3' to the
second domain.

If required, the target analyte is prepared using known techniques. For example, the sample may be
treated to lyse the cells, using known lysis buffers, electroporation, etc., with purification occuring as
30 needed, as will be appreciated by those in the art. In a preferred embodiment, when the target analyte
is nucleic acid, amplification may be done, including PCR and other amplification techniques as
outlined in PCT US99/01705, incorporated herein by reference in its entirety.

When the target analyte is a nucleic acid, probes of the present invention are designed to be
35 complementary to a target sequence (either the target sequence of the sample or to other probe

sequences, as is described below), such that hybridization of the target sequence and the probes of
the present invention occurs. As outlined below, this complementarity need not be perfect; there may

-59-

be any number of base pair mismatches which will interfere with hybridization between the target
sequence and the single stranded nucleic acids of the present invention. However, if the number of
mutations is so great that no hybridization can occur under even the least stringent of hybridization
conditions, the sequence is not a complementary target sequence. Thus, by "substantially
5 complementary" herein is meant that the probes are sufficiently complementary to the target
sequences to hybridize under normal reaction conditions.

Generally, the nucleic acid compositions of the invention are useful as oligonucleotide probes. As is
appreciated by those in the art, the length of the probe will vary with the length of the target sequence
10 and the hybridization and wash conditions. Generally, oligonucleotide probes range from about 8 to
about 50 nucleotides, with from about 10 to about 30 being preferred and from about 12 to about 25
being especially preferred. In some cases, very long probes may be used, e.g. 50 to 200-300
nucleotides in length. Thus, in the structures depicted herein, nucleosides may be replaced with
nucleic acids.

15

A variety of hybridization conditions may be used in the present invention, including high, moderate
and low stringency conditions; see for example Maniatis et al., Molecular Cloning: A Laboratory
Manual, 2d Edition, 1989, and Short Protocols in Molecular Biology, ed. Ausubel, et al, hereby
incorporated by referenece. The hybridization conditions may also vary when a non-ionic backbone,
20 i.e. PNA is used, as is known in the art. In addition, cross-linking agents may be added after target
binding to cross-link, i.e. covalently attach, the two strands of the hybridization complex.

When gold electrodes are used, a C6 insulator, comprising 6-mercaptohexanol, is included in the
hybridization buffer.

25

As will be appreciated by those in the art, the nucleic acid systems of the invention may take on a
large number of different configurations, as is generally depicted in the figures. In general, there are
three types of systems that can be used: (1) systems in which the target analyte itself is labeled with
ETMs (i.e. the use of a target analyte analog, for non-nucleic acid systems, or, for nucleic acid
30 systems, the target sequence is labeled); (2) systems in which label probes (or capture binding ligands
with recruitment linkers) directly bind (i.e. hybridize for nucleic acids) to the target analytes; and (3)
systems in which label probes comprising recruitment linkers are indirectly bound to the target
analytes, for example through the use of amplifier probes.

35 In all three of these systems, it is preferred, although not required, that the target analyte be

immobilized on the electrode surface. This is preferably done using capture binding ligands and
optionally one or more capture extender ligands. When only capture binding ligands are utilized, it is

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necessary to have unique capture binding ligands for each target analyte; that is, the surface must be
customized to contain unique capture binding ligands. Alternatively, the use of capture extender
ligands, particularly when the capture extender ligands are capture extender probes (i.e. nucleic acids)
may be used, that allow a "universal" surface, i.e. a surface containing a single type of capture probe
5 that can be used to detect any target sequence.

In a preferred embodiment, the capture binding ligands are added after the formation of the SAM ((4)
above). This may be done in a variety of ways, as will be appreciated by those in the art. In one
embodiment, conductive oligomers with terminal functional groups are made, with preferred

10 embodiments utilizing activated carboxylates and isothiocyanates, that will react with primary amines
that are put onto the binding ligand, using an activated carboxylate and nucleic acid, although other
capture ligands may be attached in this way as well. These two reagents have the advantage of being
stable in aqueous solution, yet react with primary alkylamines. This allows the spotting of probes
(either capture or detection probes, or both) using known methods (ink jet, spotting, etc.) onto the

15 surface.

In addition, there are a number of non-nucleic acid methods that can be used to immobilize a capture
binding ligand on a surface. For example, binding partner pairs can be utilized; i.e. one binding
partner is attached to the terminus of the conductive oligomer, and the other to the end of the binding

20 iigand. This may also be done without using a nucleic acid capture probe; that is, one binding partner
serves as the capture probe and the other is attached to either the target sequence or a capture
extender probe. That is, either the target sequence comprises the binding partner, or a capture
extender probe that will hybridize to the target sequence comprises the binding partner. Suitable
binding partner pairs include, but are not limited to, hapten pairs such as biotin/streptavidin;

25 antigens/antibodies; NTA/histidine tags; etc. In general, smaller binding partners are preferred.

In a preferred embodiment, when the target sequence itself is modified to contain a binding partner,
the binding partner is attached via a modified nucleotide that can be enzymatically attached to the
30 target sequence, for example during a PCR target amplification step. Alternatively, the binding partner
should be easily attached to the target sequence.

Alternatively, a capture extender probe may be utilized that has a nucleic acid portion for hybridization
to the target as well as a binding partner (for example, the capture extender probe may comprise a
35 non-nucleic acid portion such as an alkyl linker that is used to attach a binding partner). In this
embodiment, it may be desirable to cross-link the double-stranded nucleic acid of the target and
capture extender probe for stability, for example using psoralen as is known in the art.

-61 -

In one embodiment, the target is not bound to the electrode surface using capture binding ligands. In
this embodiment, what is important, as for all the assays herein, is that excess label probes be
removed prior to detection and that the assay complex (comprising the recruitment linker) be in
proximity to the surface. As will be appreciated by those in the art, this may be accomplished in other
5 ways. For example, the assay complex may be present on beads that are added to the electrode

comprising the monolayer. The recruitment linkers comprising the ETMs may be placed in proximity to
the conductive oligomer surface using techniques well known in the art, including gravity settling of the
beads on the surface, electrostatic or magnetic interactions between bead components and the
surface, using binding partner attachment as outlined above. Alternatively, after the removal of excess
10 reagents such as excess label probes, the assay complex may be driven down to the surface, for
example by pulsing the system with a voltage sufficient to drive the assay complex to the surface.

However, preferred embodiments utilize assay complexes attached via capture binding ligands.

15 For nucleic acid systems, a preferred embodiments utilize the target sequence itself containing the
ETMs. As discussed above, this may be done using target sequences that have ETMs incorporated
at any number of positions, as outlined above. In this embodiment, as for the others of the system, the
3'-5' orientation of the probes and targets is chosen to get the ETM-containing structures (i.e.
recruitment linkers or target sequences) as close to the surface of the monolayer as possible, and in

20 the correct orientation. This may be done using attachment via insulators or conductive oligomers. In
addition, as will be appreciated by those in the art, multiple capture probes can be utilized, either in a
configuration wherein the 5'-3' orientation of the capture probes is different, or where "loops" of target
form when multiples of capture probes are used.

25 For nucleic acid systems, a preferred embodiments utilize the label probes directly hybridizing to the
target sequences, as is generally depicted in Figures 7D - 71. In these embodiments, the target
sequence is preferably, but not required to be, immobilized on the surface using capture probes,
including capture extender probes. Label probes are then used to bring the ETMs into proximity of the
surface of the monolayer comprising conductive oligomers. In a preferred embodiment, multiple label

30 probes are used; that is, label probes are designed such that the portion that hybridizes to the target
sequence (labeled 41 in the figures) can be different for a number of different label probes, such that
amplification of the signal occurs, since multiple label probes can bind for every target sequence.
Thus, as depicted in the figures, n is an integer of at least one. Depending on the sensitivity desired,
the length of the target sequence, the number of ETMs per label probe, etc., preferred ranges of n are

35 from 1 to 50, with from about 1 to about 20 being particularly preferred, and from about 2 to about 5
being especially preferred. In addition, if "generic" label probes are desired, label extender probes
can be used as generally described below for use with amplifier probes.

-62-

As above, generally in this embodiment the configuration of the system and the label probes
(recruitment linkers) are designed to recruit the ETMs as close as possible to the monolayer surface.

In a preferred embodiment, the label probes are bound to the target analyte indirectly. That is, the
5 present invention finds use in novel combinations of signal amplification technologies and electron

transfer detection on electrodes, which may be particularly useful in sandwich hybridization assays, for
nucleic acid detection. In these embodiments, the amplifier probes of the invention are bound to the
target sequence in a sample either directly or indirectly. Since the amplifier probes preferably contain
a relatively large number of amplification sequences that are available for binding of label probes, the
10 detectable signal is significantly increased, and allows the detection limits of the target to be

significantly improved. These label and amplifier probes, and the detection methods described herein,
may be used in essentially any known nucleic acid hybridization formats, such as those in which the
target is bound directly to a solid phase or in sandwich hybridization assays in which the target is
bound to one or more nucleic acids that are in turn bound to the solid phase.

15

In general, these embodiments may be described as follows. An amplifier probe is hybridized to the
target sequence, either directly (e.g. Figure7l), or through the use of a label extender probe (e.g.
Figure 7N and 70), which serves to allow "generic" amplifier probes to be made. The target sequence
is preferably, but not required to be, immobilized on the electrode using capture probes. Preferably,
20 the amplifier probe contains a multiplicity of amplification sequences, although in some embodiments,
as described below, the amplifier probe may contain only a single amplification sequence. The
amplifier probe may take on a number of different forms; either a branched conformation, a dendrimer
conformation, or a linear "string" of amplification sequences. These amplification sequences are used
to form hybridization complexes with label probes, and the ETMs can be detected using the electrode.

25

Accordingly, the present invention provides assay complexes comprising at least one amplifier probe.
By "amplifier probe" or "nucleic acid multimer" or "amplification multimer" or grammatical equivalents
herein is meant a nucleic acid probe that is used to facilitate signal amplification. Amplifier probes
comprise at least a first single-stranded nucleic acid probe sequence, as defined below, and at least
30 one single-stranded nucleic acid amplification sequence, with a multiplicity of amplification sequences
being preferred. In some embodiments, it is possible to use amplifier binding ligands, that are non-
nucleic acid based but that comprise a plurality of binding sites for the later association/binding of label
ligands comprising recruitment linkers. However, amplifier probes are preferred in nucleic acid
systems.

35

Amplifier probes comprise a first probe sequence that is used, either directly or indirectly, to hybridize
to the target sequence. That is, the amplifier probe itself may have a first probe sequence that is

-63-

substantially complementary to the target sequence (e.g. Figure 71), or it has a first probe sequence
that is substantially complementary to a portion of an additional probe, in this case called a label
extender probe, that has a first portion that is substantially complementary to the target sequence (e.g.
Figure 7N). In a preferred embodiment, the first probe sequence of the amplifier probe is substantially
5 complementary to the target sequence, as is generally depicted in Figure 71.

In general, as for all the probes herein, the first probe sequence is of a length sufficient to give
specificity and stability. Thus generally, the probe sequences of the invention that are designed to
hybridize to another nucleic acid (i.e. probe sequences, amplification sequences, portions or domains
10 of larger probes) are at least about 5 nucleosides long, with at least about 10 being preferred and at
least about 15 being especially preferred.

In a preferred embodiment, the amplifier probes, or any of the other probes of the invention, may form
hairpin stem-loop structures in the absence of their target. The length of the stem double-stranded
15 sequence will be selected such that the hairpin structure is not favored in the presence of target. The
use of these type of probes, in the systems of the invention or in any nucleic acid detection systems,
can result in a significant decrease in non-specific binding and thus an increase in the signal to noise
ratio.

20 Generally, these hairpin structures comprise four components. The first component is a target binding
sequence, i.e. a region complementary to the target (which may be the sample target sequence or
another probe sequence to which binding is desired), that is about 10 nucleosides long, with about 15
being preferred. The second component is a loop sequence, that can facilitate the formation of nucleic
acid loops. Particularly preferred in this regard are repeats of GTC, which has been identified in

25 Fragile X Syndrome as forming turns. (When PNA analogs are used, turns comprising proline

residues may be preferred). Generally, from three to five repeats are used, with four to five being
preferred. The third component is a self-complementary region, which has a first portion that is
complementary to a portion of the target sequence region and a second portion that comprises a first
portion of the label probe binding sequence. The fourth component is substantially complementary to

30 a label probe (or other probe, as the case may be). The fourth component further comprises a "sticky
end", that is, a portion that does not hybridize to any other portion of the probe, and preferably
contains most, if not all, of the ETMs. As will be appreciated by those in the art, the any or all of the
probes described herein may be configured to form hairpins in the absence of their targets, including
the amplifier, capture, capture extender, label and label extender probes.

35

in a preferred embodiment, several different amplifier probes are used, each with first probe
sequences that will hybridize to a different portion of the target sequence. That is, there is more than

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one level of amplification; the amplifier probe provides an amplification of signal due to a multiplicity of
labelling events, and several different amplifier probes, each with this multiplicity of labels, for each
target sequence is used. Thus, preferred embodiments utilize at least two different pools of amplifier
probes, each pool having a different probe sequence for hybridization to different portions of the target
5 sequence; the only real limitation on the number of different amplifier probes will be the length of the
original target sequence. In addition, it is also possible that the different amplifier probes contain
different amplification sequences, although this is generally not preferred.

In a preferred embodiment, the amplifier probe does not hybridize to the sample target sequence
10 directly, but instead hybridizes to a first portion of a label extender probe, as is generally depicted in
Figure7L This is particularly useful to allow the use of "generic" amplifier probes, that is, amplifier
probes that can be used with a variety of different targets. This may be desirable since several of the
amplifier probes require special synthesis techniques. Thus, the addition of a relatively short probe as
a label extender probe is preferred. Thus, the first probe sequence of the amplifier probe is
15 substantially complementary to a first portion or domain of a first label extender single-stranded
nucleic acid probe. The label extender probe also contains a second portion or domain that is
substantially complementary to a portion of the target sequence. Both of these portions are preferably
at least about 10 to about 50 nucleotides in length, with a range of about 15 to about 30 being
preferred. The terms "first" and "second" are not meant to confer an orientation of the sequences with
20 respect to the 5'-3' orientation of the target or probe sequences. For example, assuming a 5'-3'
orientation of the complementary target sequence, the first portion may be located either 5' to the
second portion, or 3' to the second portion. For convenience herein, the order of probe sequences are
generally shown from left to right.

25 In a preferred embodiment, more than one label extender probe-amplifier probe pair may be used, tht
is, n is more than 1 . That is, a plurality of label extender probes may be used, each with a portion that
is substantially complementary to a different portion of the target sequence; this can serve as another
level of amplification. Thus, a preferred embodiment utilizes pools of at least two label extender
probes, with the upper limit being set by the length of the target sequence.

30

In a preferred embodiment, more than one label extender probe is used with a single amplifier probe to
reduce non-specific binding, as is depicted in Figure 70 and generally outlined in U.S. Patent No.
5,681,697, incorporated by reference herein. In this embodiment, a first portion of the first label
extender probe hybridizes to a first portion of the target sequence, and the second portion of the first
35 label extender probe hybridizes to a first probe sequence of the amplifier probe. A first portion of the
second label extender probe hybridizes to a second portion of the target sequence, and the second
portion of the second label extender probe hybridizes to a second probe sequence of the amplifier

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probe. These form structures sometimes referred to as "cruciform" structures or configurations, and
are generally done to confer stability when large branched or dendrimeric amplifier probes are used.

In addition, as will be appreciated by those in the art, the label extender probes may interact with a
5 preamplifier probe, described below, rather than the amplifier probe directly.

Similarly, as outlined above, a preferred embodiment utilizes several different amplifier probes, each
with first probe sequences that will hybridize to a different portion of the label extender probe. In
addition, as outlined above, it is also possible that the different amplifier probes contain different
10 amplification sequences, although this is generally not preferred.

In addition to the first probe sequence, the amplifier probe also comprises at least one amplification
sequence. An "amplification sequence" or "amplification segment" or grammatical equivalents herein
is meant a sequence that is used, either directly or indirectly, to bind to a first portion of a label probe

15 as is more fully described below. Preferably, the amplifier probe comprises a multiplicity of

amplification sequences, with from about 3 to about 1000 being preferred, from about 10 to about 100
being particularly preferred, and about 50 being especially preferred. In some cases, for example
when linear amplifier probes are used, from 1 to about 20 is preferred with from about 5 to about 10
being particularly preferred. Again, when non-nucleic acid amplifier moieties are used, the

20 amplification segment can bind label ligands.

The amplification sequences may be linked to each other in a variety of ways, as will be appreciated
by those in the art. They may be covalently linked directly to each other, or to intervening sequences
or chemical moieties, through nucleic acid linkages such as phosphodiester bonds, PNA bonds, etc.,
25 or through interposed linking agents such amino acid, carbohydrate or polyol bridges, or through other
cross-linking agents or binding partners. The site(s) of linkage may be at the ends of a segment,
and/or at one or more internal nucleotides in the strand. In a preferred embodiment, the amplification
sequences are attached via nucleic acid linkages.

30 In a preferred embodiment, branched amplifier probes are used, as are generally described in U.S.
Patent No. 5,124,246, hereby incorporated by reference. Branched amplifier probes may take on
"fork-like" or "comb-like" conformations. "Fork-like" branched amplifier probes generally have three or
more oligonucleotide segments emanating from a point of origin to form a branched structure. The
point of origin may be another nucleotide segment or a multifunctional molecule to whcih at least three

35 segments can be covalently or tightly bound. "Comb-iike" branched amplifier probes have a linear
backbone with a multiplicity of sidechain oligonucleotides extending from the backbone. In either
conformation, the pendant segments will normally depend from a modified nucleotide or other organic

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moiety having the appropriate functional groups for attachment of oligonucleotides. Furthermore, in
either conformation, a large number of amplification sequences are available for binding, either directly
or indirectly, to detection probes. In general, these structures are made as is known in the art, using
modified multifunctional nucleotides, as is described in U.S. Patent Nos. 5,635,352 and 5,124,246,
5 among others.

In a preferred embodiment, dendrimer amplifier probes are used, as are generally described in U.S.
Patent No. 5,175,270, hereby expressly incorporated by reference. Dendrimeric amplifier probes have
amplification sequences that are attached via hybridization, and thus have portions of double-stranded
10 nucleic acid as a component of their structure. The outer surface of the dendrimer amplifier probe has
a multiplicity of amplification sequences.

In a preferred embodiment, linear amplifier probes are used, that have individual amplification
sequences linked end-to-end either directly or with short intervening sequences to form a polymer. As
15 with the other amplifier configurations, there may be additional sequences or moieties between the
amplification sequences. In addition, as outlined herein, linear amplification probes may form hairpin
stem-loop structures.

In one embodiment, the linear amplifier probe has a single amplification sequence. This may be useful
20 when cycles of hybridization/disassociation occurs, forming a pool of amplifier probe that was

hybridized to the target and then removed to allow more probes to bind, or when large numbers of
ETMs are used for each label probe. However, in a preferred embodiment, linear amplifier probes
comprise a multiplicity of amplification sequences.

25 In addition, the amplifier probe may be totally linear, totally branched, totally dendrimeric, or any
combination thereof.

The amplification sequences of the amplifier probe are used, either directly or indirectly, to bind to a
label probe to allow detection. In a preferred embodiment, the amplification sequences of the
30 amplifier probe are substantially complementary to a first portion of a label probe. Alternatively,

amplifier extender probes are used, that have a first portion that binds to the amplification sequence
and a second portion that binds to the first portion of the label probe.

In addition, the compositions of the invention may include "preamplifier" molecules, which serves a
35 bridging moiety between the label extender molecules and the amplifier probes. In this way, more
amplifier and thus more ETMs are ultimately bound to the detection probes. Preamplifier molecules
may be either linear or branched, and typically contain in the range of about 30-3000 nucleotides.

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The reactions outlined below may be accomplished in a variety of ways, as will be appreciated by
those in the art. Components of the reaction may be added simultaneously, or sequentially, in any
order, with preferred embodiments outlined below. In addition, the reaction may include a variety of
other reagents may be included in the assays. These include reagents like salts, buffers, neutral
5 proteins, e.g. albumin, detergents, etc which may be used to facilitate optimal hybridization and
detection, and/or reduce non-specific or background interactions. Also reagents that otherwise
improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial
agents, etc., may be used, depending on the sample preparation methods and purity of the target.

10 Generally, the methods are as follows. In a preferred embodiment, the target is initially immobilized or
attached to the electrode. For nucleic acids, this is done by forming a hybridization complex between
a capture probe and a portion of the target sequence. A preferred embodiment utilizes capture
extender probes; in this embodiment, a hybridization complex is formed between a portion of the
target sequence and a first portion of a capture extender probe, and an additional hybridization

15 complex between a second portion of the capture extender probe and a portion of the capture probe.
Additional preferred embodiments utilize additional capture probes, thus forming a hybridization
complex between a portion of the target sequence and a first portion of a second capture extender
probe, and an additional hybridization complex between a second portion of the second capture
extender probe and a second portion of the capture probe. Non-nucleic acid embodiments utilize

20 capture binding ligands and optional capture extender ligands.

Alternatively, the attachment of the target sequence to the electrode is done simultaneously with the
other reactions.

25 The method proceeds with the introduction of amplifier probes, if utilized. In a preferred embodiment,
the amplifier probe comprises a first probe sequence that is substantially complementary to a portion
of the target sequence, and at least one amplification sequence.

In one embodiment, the first probe sequence of the amplifier probe is hybridized to the target
30 sequence, and any unhybridized amplifier probe is removed. This will generally be done as is known
in the art, and depends on the type of assay. When the target sequence is immobilized on a surface
such as an electrode, the removal of excess reagents generally is done via one or more washing
steps, as will be appreciated by those in the art. In this embodiment, the target may be immobilized on
any solid support. When the target sequence is not immobilized on a surface, the removal of excess
35 reagents such as the probes of the invention may be done by adding beads (i.e. solid support

particles) that contain complementary sequences to the probes, such that the excess probes bind to

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the beads. The beads can then be removed, for example by centrifugation, filtration, the application of
magnetic or electrostatic fields, etc.

The reaction mixture is then subjected to conditions (temperature, high salt, changes in pH, etc.) under
5 which the amplifier probe disassociates from the target sequence, and the amplifier probe is collected.
The amplifier probe may then be added to an electrode comprising capture probes for the amplifier
probes, label probes added, and detection is achieved.

In a preferred embodiment, a larger pool of probe is generated by adding more amplifier probe to the
10 target sequence and the hybridization/disassociation reactions are repeated, to generate a larger pool
of amplifier probe. This pool of amplifier probe is then added to an electrode comprising amplifier
capture probes, label probes added, and detection proceeds.

In this embodiment, it is preferred that the target analyte be immobilized on a solid support, including
15 an electrode, using the methods described herein; although as will be appreciated by those in the art,
alternate solid support attachment technologies may be used, such as attachment to glass, polymers,
etc. It is possible to do the reaction on one solid support and then add the pooled amplifier probe to an
electrode for detection.

20 In a preferred embodiment, the amplifier probe comprises a multiplicity of amplification sequences.

In one embodiment, the first probe sequence of the amplifier probe is hybridized to the target
sequence, and any unhybridized amplifier probe is removed. Again, preferred embodiments utilize
immobilized target sequences, wherein the target sequences are immobilized by hybridization with
25 capture probes that are attached to the electrode, or hybridization to capture extender probes that in
turn hybridize with immobilized capture probes as is described herein. Generally, in these
embodiments, the capture probes and the detection probes are immobilized on the electrode,
generally at the same "address".

30 In a preferred embodiment, the first probe sequence of the amplifier probe is hybridized to a first
portion of at least one label extender probe, and a second portion of the label extender probe is
hybridized to a portion of the target sequence. Other preferred embodiments utilize more than one
label extender probe, as is generally shown in Figure 70.

35 In a preferred embodiment, the amplification sequences of the amplifier probe are used directly for
detection, by hybridizing at least one label probe sequence.

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The invention thus provides assay complexes that minimally comprise a target sequence and a label
probe. "Assay complex" herein is meant the collection of binding complexes comprising capture
binding ligands, target analytes (or analogs, as described below) and label moieties comprising
recruitment linkers that allows detection. The composition of the assay complex depends on the use
5 of the different components outlined herein. Thus, the assay complex comprises the capture probe
and the target sequence. The assay complexes may also include capture extender ligands (including
probes), label extender ligands, and amplifier ligands, as outlined herein, depending on the
configuration used.

10 The assays are generally run under conditions which allows formation of the assay complex only in
the presence of target. Stringency can be controlled by altering a step parameter that is a
thermodynamic variable, including, but not limited to, temperature, formamide concentration, salt
concentration, chaotropic salt concentration pH, organic solvent concentration, etc.

15 These parameters may also be used to control non-specific binding for nucleic acids, as is generally
outlined in U.S. Patent No. 5,681 ,697. Thus it may be desirable to perform certain steps at higher
stringency conditions; for example, when an initial hybridization step is done between the target
sequence and the label extender and capture extender probes. Running this step at conditions which
favor specific binding can allow the reduction of non-specific binding.

20

In a preferred embodiment, when all of the components outlined herein are used, a preferred method
for nucleic acid detection is as follows. Single-stranded target sequence is incubated under
hybridization conditions with the capture extender probes and the label extender probes. A preferred
embodiment does this reaction in the presence of the electrode with immobilized capture probes,
25 although this may also be done in two steps, with the initial incubation and the subsequent addition to
the electrode. Excess reagents are washed off, and amplifier probes are then added. If preamplifier
probes are used, they may be added either prior to the amplifier probes or simultaneously with the
amplifier probes. Excess reagents are washed off, and label probes are then added. Excess
reagents are washed off, and detection proceeds as outlined below.

30

In one embodiment, a number of capture probes (or capture probes and capture extender probes) that
are each substantially complementary to a different portion of the target sequence are used.

Again, as outlined herein, when amplifier probes are used, the system is generally configured such
35 that upon label probe binding, the recruitment linkers comprising the ETMs are placed in proximity to
the monolayer surface. Thus for example, when the ETMs are attached via "dendrimer" type
structures as outlined herein, the length of the linkers from the nucleic acid point of attachment to the

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ETMs may vary, particularly with the length of the capture probe when capture extender probes are
used. That is, longer capture probes, with capture extenders, can result in the target sequences being
"held" further away from the surface than for shorter capture probes. Adding extra linking sequences
between the probe nucleic acid and the ETMs can result in the ETMs being spatially closer to the
5 surface, giving better results.

In addition, if desirable, nucleic acids utilized in the invention may also be ligated together prior to
detection, if applicable, by using standard molecular biology techniques such as the use of a ligase.
Similarly, if desirable for stability, cross-linking agents may be added to hold the structures stable.

10

Other embodiments of the invention utilize different steps. For example, competitive assays may be
run. In this embodiment, the target analyte in a sample may be replaced by a target analyte analog
comprising a portion that either comprises a recruitment linker or can indirectly bind a recruitment
linker. This may be done as is known in the art, for example by using affinity chromatography
15 techniques that exchange the analog for the analyte, leaving the analyte bound and the analog free to
interact with the capture binding ligands on the electrode surface. This is generally depicted in Figure
6A.

Alternatively, a preferred embodiment utilizes a competitive binding assay when the solution binding
20 ligand comprises a directly or indirectly associated recruitment linker comprising ETMs. In this
embodiment, a target analyte or target analyte analog that will bind the solution binding ligand is
attached to the surface. The solution binding ligand will bind to the surface bound analyte and give a
signal. Upon introduction of the target analyte of the sample, a proportion of the solution binding
ligand will dissociate from the surface bound target and bind to the incoming target analyte. Thus, a
25 loss of signal proportional to the amount of target analyte in the sample is seen.

The compositions of the invention are generally synthesized as outlined below, generally utilizing
techniques well known in the art. As will be appreciated by those in the art, many of the techniques
outlined below are directed to nucleic acids containing a ribose-phosphate backbone. However, as
30 outlined above, many alternate nucleic acid analogs may be utilized, some of which may not contain
either ribose or phosphate in the backbone. In these embodiments, for attachment at positions other
than the base, attachment is done as will be appreciated by those in the art, depending on the
backbone. Thus, for example, attachment can be made at the carbon atoms of the PMA backbone, as
is described below, or at either terminus of the PNA.

35

The compositions may be made in several ways. A preferred method first synthesizes a conductive
oligomer attached to a nucleoside, with addition of additional nucleosides to form the capture probe

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followed by attachment to the electrode. Alternatively, the whole capture probe may be made and
then the completed conductive oligomer added, followed by attachment to the electrode. Alternatively,
a monolayer of conductive oligomer (some of which have functional groups for attachment of capture
probes) is attached to the electrode first, followed by attachment of the capture probe. The latter two
5 methods may be preferred when conductive oligomers are used which are not stable in the solvents
and under the conditions used in traditional nucleic acid synthesis.

In a preferred embodiment, the compositions of the invention are made by first forming the conductive
oligomer covalently attached to the nucleoside, followed by the addition of additional nucleosides to
1 0 form a capture probe nucleic acid, with the last step comprising the addition of the conductive oligomer
to the electrode.

The attachment of the conductive oligomer to the nucleoside may be done in several ways. In a
preferred embodiment, all or part of the conductive oligomer is synthesized first (generally with a

15 functional group on the end for attachment to the electrode), which is then attached to the nucleoside.
Additional nucleosides are then added as required, with the last step generally being attachment to the
electrode. Alternatively, oligomer units are added one at a time to the nucleoside, with addition of
additional nucleosides and attachment to the electrode. A number of representative syntheses are
shown in the Figures of WO 98/20162, PCT US98/12430, PCT US99/01705 and PCT US99/01703, all

20 of which are expressly incorporated by reference.

The conductive oligomer is then attached to a nucleoside that may contain one (or more) of the
oligomer units, attached as depicted herein.

25 In a preferred embodiment, attachment is to a ribose of the ribose-phosphate backbone in a number of
ways, including attachment via amide and amine linkages. In a preferred embodiment, there is at least
a methylene group or other short aliphatic alkyl groups (as a Z group) between the nitrogen attached
to the ribose and the aromatic ring of the conductive oligomer.

30 Alternatively, attachment is via a phosphate of the ribose-phosphate backbone.

In a preferred embodiment, attachment is via the base, and can include acetylene linkages and amide
linkages. In a preferred embodiment, protecting groups may be added to the base prior to addition of
the conductive oligomers. In addition, the palladium cross-coupling reactions may be altered to
35 prevent dimerization problems; i.e. two conductive oligomers dimerizing, rather than coupling to the
base.

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Alternatively, attachment to the base may be done by making the nucleoside with one unit of the
oligomer, followed by the addition of others.

Once the modified nucleosides are prepared, protected and activated, prior to attachment to the
5 electrode, they may be incorporated into a growing oligonucleotide by standard synthetic techniques
(Gait, Oligonucleotide Synthesis: A Practical Approach, IRL Press, Oxford, UK 1984; Eckstein) in
several ways.

In one embodiment, one or more modified nucleosides are converted to the triphosphate form and
10 incorporated into a growing oligonucleotide chain by using standard molecular biology techniques
such as with the use of the enzyme DNA polymerase I, T4 DNA polymerase, 17 DNA polymerase,
Taq DNA polymerase, reverse transcriptase, and RNA polymerases. For the incorporation of a 3'
modified nucleoside to a nucleic acid, terminal deoxynucleotidyltransferase may be used. (Ratliff,
Terminal deoxynucleotidyltransferase. In The Enzymes, Vol 14A. P.D. Boyered. pp 105-118.
15 Academic Press, San Diego, CA. 1981). Thus, the present invention provides deoxyribonucleoside

triphosphates comprising a covalently attached ETM. Preferred embodiments utilize ETM attachment
to the base or the backbone, such as the ribose (preferably in the 2' position), as is generally depicted
below in Structures 42 and 43:

Structure 42

20

25

30

Structure 43

35 Thus, in some embodiments, it may be possible to generate the nucleic acids comprising ETMs in situ.
For example, a target sequence can hybridize to a capture probe (for example on the surface) in such
a way that the terminus of the target sequence is exposed, i.e. unhybridized. The addition of enzyme

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and triphosphate nucleotides labelled with ETMs allows the in situ creation of the label. Similarly,
using labeled nucleotides recognized by polymerases can allow simultaneous PCR and detection; that
is, the target sequences are generated in situ.

5 In a preferred embodiment, the modified nucleoside is converted to the phosphoramidite or H-

phosphonate form, which are then used in solid-phase or solution syntheses of oligonucleotides. In
this way the modified nucleoside, either for attachment at the ribose (i.e. amino- or thiol-modified
nucleosides) or the base, is incorporated into the oligonucleotide at either an internal position or the 5'
terminus. This is generally done in one of two ways. First, the 5' position of the ribose is protected

10 with 4',4-dimethoxytrityl (DMT) followed by reaction with either 2-cyanoethoxy-bis-

diisopropylaminophosphine in the presence of diisopropylammonium tetrazolide, or by reaction with
chlorodiisopropylamino 2'-cyanoethyoxyphosphine, to give the phosphoramidite as is known in the
art; although other techniques may be used as will be appreciated by those in the art. See Gait,
supra; Caruthers, Science 230:281 (1985), both of which are expressly incorporated herein by

1 5 reference.

For attachment of a group to the 3' terminus, a preferred method utilizes the attachment of the
modified nucleoside (or the nucleoside replacement) to controlled pore glass (CPG) or other
oligomeric supports. In this embodiment, the modified nucleoside is protected at the 5' end with DMT,
20 and then reacted with succinic anhydride with activation. The resulting succinyl compound is attached
to CPG or other oligomeric supports as is known in the art. Further phosphoramidite nucleosides are
added, either modified or not, to the 5' end after deprotection. Thus, the present invention provides
conductive oligomers or insulators covalently attached to nucleosides attached to solid oligomeric
supports such as CPG, and phosphoramidite derivatives of the nucleosides of the invention.

25

The invention further provides methods of making label probes with recruitment linkers comprising
ETMs. These synthetic reactions will depend on the character of the recruitment linker and the
method of attachment of the ETM, as will be appreciated by those in the art. For nucleic acid
recruitment linkers, the label probes are generally made as outlined herein with the incorporation of

30 ETMs at one or more positions. When a transition metal complex is used as the ETM, synthesis may
occur in several ways. In a preferred embodiment, the ligand(s) are added to a nucleoside, followed
by the transition metal ion, and then the nucleoside with the transition metal complex attached is
added to an oligonucleotide, i.e. by addition to the nucleic acid synthesizer. Alternatively, the
ligand(s) may be attached, followed by incorportation into a growing oligonucleotide chain, followed by

35 the addition of the metal ion.

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In a preferred embodiment, ETMs are attached to a ribose of the ribose-phosphate backbone. This is
generally done as is outlined herein for conductive oligomers, as described herein, and in PCT
publication WO 95/1 5971 , using amino-modified or oxo-modified nucleosides, at either the 2' or 3'
position of the ribose. The amino group may then be used either as a ligand, for example as a
5 transition metal ligand for attachment of the metal ion, or as a chemically functional group that can be
used for attachment of other ligands or organic ETMs, for example via amide linkages, as will be
appreciated by those in the art. For example, the examples describe the synthesis of nucleosides with
a variety of ETMs attached via the ribose.

10 In a preferred embodiment, ETMs are attached to a phosphate of the ribose-phosphate backbone. As
outlined herein, this may be done using phosphodiester analogs such as phosphoramidite bonds, see
generally PCT publication WO 95/15971, or the figures.

Attachment to alternate backbones, for example peptide nucleic acids or alternate phosphate linkages
15 will be done as will be appreciated by those in the art.

In a preferred embodiment, ETMs are attached to a base of the nucleoside. This may be done in a
variety of ways. In one embodiment, amino groups of the base, either naturally occurring or added as
is described herein (see the figures, for example), are used either as ligands for transition metal

20 complexes or as a chemically functional group that can be used to add other ligands, for example via
an amide linkage, or organic ETMs. This is done as will be appreciated by those in the art.
Alternatively, nucleosides containing halogen atoms attached to the heterocyclic ring are commercially
available. Acetylene linked ligands may be added using the halogenated bases, as is generally
known; see for example, Tzalis et al., Tetrahedron Lett. 36(34):601 7-6020 (1995); Tzalis et al.,

25 Tetrahedron Lett. 36 (2): 3489-3490 (1995); and Tzalis et al., Chem. Communications (in press) 1996,
all of which are hereby expressly incorporated by reference. See also PCT/US99/10104 which
describes the synthesis of metallocenes (in this case, ferrocene) attached via acetylene linkages to
the bases.

30 in one embodiment, the nucleosides are made with transition metal ligands, incorporated into a nucleic
acid, and then the transition metal ion and any remaining necessary ligands are added as is known in
the art. In an alternative embodiment, the transition metal ion and additional ligands are added prior to
incorporation into the nucleic acid.

35 Once the nucleic acids of the invention are made, with a covaiently attached attachment linker (i.e.

either an insulator or a conductive oligomer), the attachment linker is attached to the electrode. The
method will vary depending on the type of electrode used. As is described herein, the attachment

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linkers are generally made with a terminal "A" linker to facilitate attachment to the electrode. For the
purposes of this application, a sulfur-gold attachment is considered a covalent attachment.

In a preferred embodiment, conductive oligomers, insulators, and attachment linkers are covalently
5 attached via sulfur linkages to the electrode. However, surprisingly, traditional protecting groups for
use of attaching molecules to gold electrodes are generally not ideal for use in both synthesis of the
compositions described herein and inclusion in oligonucleotide synthetic reactions. Accordingly, the
present invention provides novel methods for the attachment of conductive oligomers to gold
electrodes, utilizing unusual protecting groups, including ethylpyridine, and trimethylsilylethyl.
10 However, as will be appreciated by those in the art, when the conductive oligomers do not contain
nucleic acids, traditional protecting groups such as acetyl groups and others may be used. See
Greene et al., supra.

This may be done in several ways. In a preferred embodiment, the subunit of the conductive oligomer
15 which contains the sulfur atom for attachment to the electrode is protected with an ethyl-pyridine or

trimethylsilylethyl group. For the former, this is generally done by contacting the subunit containing the
sulfur atom (preferably in the form of a sulfhydryl) with a vinyl pyridine group or vinyl trimethylsilylethyl
group under conditions whereby an ethylpyridine group or trimethylsilylethyl group is added to the
sulfur atom.

20

This subunit also generally contains a functional moiety for attachment of additional subunits, and thus
additional subunits are attached to form the conductive oligomer. The conductive oligomer is then
attached to a nucleoside, and additional nucleosides attached. The protecting group is then removed
and the sulfur-gold covalent attachment is made. Alternatively, all or part of the conductive oligomer is

25 made, and then either a subunit containing a protected sulfur atom is added, or a sulfur atom is added
and then protected. The conductive oligomer is then attached to a nucleoside, and additional
nucleosides attached. Alternatively, the conductive oligomer attached to a nucleic acid is made, and
then either a subunit containing a protected sulfur atom is added, or a sulfur atom is added and then
protected. Alternatively, the ethyl pyridine protecting group may be used as above, but removed after

30 one or more steps and replaced with a standard protecting group like a disulfide. Thus, the ethyl
pyridine or trimethylsilylethyl group may serve as the protecting group for some of the synthetic
reactions, and then removed and replaced with a traditional protecting group.

By "subunit" of a conductive polymer herein is meant at least the moiety of the conductive oligomer to
35 which the sulfur atom is attached, although additional atoms may be present, including either

functional groups which allow the addition of additional components of the conductive oligomer, or

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additional components of the conductive oligomer. Thus, for example, when Structure 1 oligomers are
used, a subunit comprises at least the first Y group.

A preferred method comprises 1) adding an ethyl pyridine or trimethylsilylethyl protecting group to a
5 sulfur atom attached to a first subunit of a conductive oligomer, generally done by adding a vinyl

pyridine or trimethylsilylethyl group to a sulfhydryl; 2) adding additional subunits to form the conductive
oligomer; 3) adding at least a first nucleoside to the conductive oligomer; 4) adding additional
nucleosides to the first nucleoside to form a nucleic acid; 5) attaching the conductive oligomer to the
gold electrode. This may also be done in the absence of nucleosides.

10

The above methods may also be used to attach insulator molecules to a gold electrode, and moieties
comprising capture binding ligands.

In a preferred embodiment, a monolayer comprising conductive oligomers (and preferably insulators)
15 is added to the electrode. Generally, the chemistry of addition is similar to or the same as the addition
of conductive oligomers to the electrode, i.e. using a sulfur atom for attachment to a gold electrode,
etc. Compositions comprising monolayers in addition to the conductive oligomers covalently attached
to nucleic acids may be made in at least one of five ways: (1) addition of the monolayer, followed by
subsequent addition of the attachment linker-nucleic acid complex; (2) addition of theattachment
20 linker-nucleic acid complex followed by addition of the monolayer; (3) simultaneous addition of the

monolayer and attachment linker-nucleic acid complex; (4) formation of a monolayer (using any of 1, 2
or 3) which includes attachment linkers which terminate in a functional moiety suitable for attachment
of a completed nucleic acid; or (5) formation of a monolayer which includes attachment linkers which
terminate in a functional moiety suitable for nucleic acid synthesis, i.e. the nucleic acid is synthesized
25 on the surface of the monolayer as is known in the art. Such suitable functional moieties include, but
are not limited to, nucleosides, amino groups, carboxyl groups, protected sulfur moieties, or hydroxyl
groups for phosphoramidite additions. The examples describe the formation of a monolayer on a gold
electrode using the preferred method (1).

30 In a preferred embodiment, the nucleic acid is a peptide nucleic acid or analog. In this embodiment,
the invention provides peptide nucleic acids with at least one covalently attached ETM or attachment
linker. In a preferred embodiment, these moieties are covalently attached to an monomeric subunit of
the PNA. By "monomeric subunit of PNA" herein is meant the -NH-CH 2 CH 2 -N(COCH 2 -Base)-CH 2 -CO-
monomer, or derivatives (herein included within the definition of "nucleoside") of PNA. For example,

35 the number of carbon atoms in the PNA backbone may be altered; see generally Nielsen et al., Chem.
Soc. Rev. 1997 page 73, which discloses a number of PNA derivatives, herein expressly incorporated
by reference. Similarly, the amide bond linking the base to the backbone may be altered;

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phosphoramide and sulfuramide bonds may be used. Alternatively, the moieties are attached to an
internal monomeric subunit. By "internal" herein is meant that the monomeric subunit is not either the
N-terminal monomeric subunit or the C-terminal monomeric subunit. In this embodiment, the moieties
can be attached either to a base or to the backbone of the monomeric subunit. Attachment to the
5 base is done as outlined herein or known in the literature. In general, the moieties are added to a

base which is then incorporated into a PNA as outlined herein. The base may be either protected, as
required for incorporation into the PNA synthetic reaction, or derivatized, to allow incorporation, either
prior to the addition of the chemical substituent or afterwards. The bases can then be incorporated
into monomeric subunits.

10

In a preferred embodiment, the moieties are covalently attached to the backbone of the PNA
monomer. The attachment is generally to one of the unsubstituted carbon atoms of the monomeric
subunit, preferably the a-carbon of the backbone, although attachment at either of the carbon 1 or 2
positions, or the a-carbon of the amide bond linking the base to the backbone may be done. In the
15 case of PNA analogs, other carbons or atoms may be substituted as well. In a preferred embodiment,
moieties are added at the a-carbon atoms, either to a terminal monomeric subunit or an internal one.

In this embodiment, a modified monomeric subunit is synthesized with an ETM or an attachment
linker, or a functional group for its attachment, and then the base is added and the modified monomer
20 can be incorporated into a growing PNA chain.

Once generated, the monomeric subunits with covalently attached moieties are incorporated into a
PNA using the techniques outlined in Will etal., Tetrahedron 51 (44): 12069-1 2082 (1995), and
Vanderlaan et a!., Tett. Let. 38:2249-2252 (1997), both of which are hereby expressly incorporated in
25 their entirety. These procedures allow the addition of chemical substituents to peptide nucleic acids
without destroying the chemical substituents.

As will be appreciated by those in the art, electrodes may be made that have any combination of
nucleic acids, conductive oligomers and insulators.

30

The compositions of the invention may additionally contain one or more labels at any position. By
"label" herein is meant an element (e.g. an isotope) or chemical compound that is attached to enable
the detection of the compound. Preferred labels are radioactive isotopic labels, and colored or
fluorescent dyes. The labels may be incorporated into the compound at any position. In addition, the
35 compositions of the invention may also contain other moieties such as cross-linking agents to facilitate
cross-linking of the target-probe complex. See for example, Lukhtanov et al., Nucl. Acids. Res.

-78 -

24(4):683 (1996) and Tabone et a!., Biochem. 33:375 (1994), both of which are expressly incorporated
by reference.

Once made, the compositions find use in a number of applications, as described herein. In particular,
5 the compositions of the invention find use in target analyte assays. As will be appreciated by those in
the art, electrodes can be made that have a single species of binding ligands such as nucleic acid, i.e.
a single binding ligand, or multiple binding ligand species.

In addition, as outlined herein, the use of a solid support such as an electrode enables the use of
10 these probes in an array form. The use of oligonucleotide arrays are well known in the art, and the
methods and compositions herein allow the use of array formats for other target analytes as well. In
addition, techniques are known for "addressing" locations within an electrode and for the surface
modification of electrodes. Thus, in a preferred embodiment, arrays of different binding ligands are
laid down on the electrode, each of which are covalently attached to the electrode via a conductive
15 linker. In this embodiment, the number of different species may vary widely, from one to thousands,
with from about 4 to about 100,000 being preferred, and from about 10 to about 10,000 being
particularly preferred.

The invention finds use in the screening of candidate bioactive agents for therapeutic agents that can
20 alter the binding of the analyte to the binding ligand, and thus may be involved in biological function.
The term "agent" or "exogeneous compound" as used herein describes any molecule, e.g., protein,
oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., with the capability of
directly or indirectly altering target analyte binding. Generally a plurality of assay mixtures are run in
parallel with different agent concentrations to obtain a differential response to the various
25 concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero
concentration or below the level of detection.

Candidate agents encompass numerous chemical classes, though typically they are organic
molecules, preferably small organic compounds having a molecular weight of more than 100 and less

30 than about 2,500 daltons. Candidate agents comprise functional groups necessary for structural
interaction with proteins, particularly hydrogen bonding, and typically include at least an amine,
carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The
candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or
polyaromatic structures substituted with one or more of the above functional groups. Candidate

35 agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids,

purines, pyrimidines, derivatives, structural analogs or combinations thereof. Particularly preferred are
peptides.

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Candidate agents are obtained from a wide variety of sources including libraries of synthetic or natural
compounds. For example, numerous means are available for random and directed synthesis of a
wide variety of organic compounds and biomolecules, including expression of randomized
oligonucleotides. Alternatively, libraries of natural compounds in the form of bacterial, fungai, plant
5 and animal extracts are available or readily produced. Additionally, natural or synthetically produced
libraries and compounds are readily modified through conventional chemical, physical and biochemical
means. Known pharmacological agents may be subjected to directed or random chemical
modifications, such as acylation, alkylation, esterification, amidification to produce structural analogs.

1 0 Candidate agents may be added either before or after the target analyte.

Once the assay complexes of the invention are made, that minimally comprise a target sequence and
a label probe, detection proceeds with electronic initiation. Without being limited by the mechanism or
theory, detection is based on the transfer of electrons from the ETM to the electrode.

15

Detection of electron transfer, i.e. the presence of the ETMs, is generally initiated electronically, with
voltage being preferred. A potential is applied to the assay complex. Precise control and variations in
the applied potential can be via a potentiostat and either a three electrode system (one reference, one
sample (or working) and one counter electrode) or a two electrode system (one sample and one
20 counter electrode). This allows matching of applied potential to peak potential of the system which
depends in part on the choice of ETMs and in part on the conductive oligomer used, the composition
and integrity of the monolayer, and what type of reference electrode is used. As described herein,
ferrocene is a preferred ETM.

25 In a preferred embodiment, a co-reductant or co-oxidant (collectively, co-redoxant) is used, as an
additional electron source or sink. See generally Sato et al., Bull. Chem. Soc. Jpn 66:1032 (1993);
Uosaki et al., Electrochi mica Acta 36:1799 (1991); and Alleman etal., J. Phys. Chem 100:17050
(1996); all of which are incorporated by reference.

30 In a preferred embodiment, an input electron source in solution is used in the initiation of electron
transfer, preferably when initiation and detection are being done using DC current or at AC
frequencies where diffusion is not limiting. In general, as will be appreciated by those in the art,
preferred embodiments utilize monolayers that contain a minimum of "holes", such that short-circuiting
of the system is avoided. This may be done in several general ways. In a preferred embodiment, an

35 input electron source is used that has a lower or similar redox potential than the ETM of the label

probe. Thus, at voltages above the redox potential of the input electron source, both the ETM and the
input electron source are oxidized and can thus donate electrons; the ETM donates an electron to the

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electrode and the input source donates to the ETM. For example, ferrocene, as a ETM attached to the
compositions of the invention as described in the examples, has a redox potential of roughly 200 mV
in aqueous solution (which can change significantly depending on what the ferrocene is bound to, the
manner of the linkage and the presence of any substitution groups). Ferrocyanide, an electron

5 source, has a redox potential of roughly 200 mV as well (in aqueous solution). Accordingly, at or
above voltages of roughly 200 mV, ferrocene is converted to ferricenium, which then transfers an
electron to the electrode. Now the ferricyanide can be oxidized to transfer an electron to the ETM. In
this way, the electron source (or co-reductant) serves to amplify the signal generated in the system, as
the electron source molecules rapidly and repeatedly donate electrons to the ETM attached to the

10 nucleic acid. The rate of electron donation or acceptance will be limited by the rate of diffusion of the
co-reductant, the electron transfer between the co-reductant and the ETM, which in turn is affected by
the concentration and size, etc.

Alternatively, input electron sources that have lower redox potentials than the ETM are used. At
15 voltages less than the redox potential of the ETM, but higher than the redox potential of the electron
source, the input source such as ferrocyanide is unable to be oxided and thus is unable to donate an
electron to the ETM; i.e. no electron transfer occurs. Once ferrocene is oxidized, then there is a
pathway for electron transfer.

20 In an alternate preferred embodiment, an input electron source is used that has a higher redox
potential than the ETM of the label probe. For example, luminol, an electron source, has a redox
potential of roughly 720 mV. At voltages higher than the redox potential of the ETM, but lower than the
redox potential of the electron source, i.e. 200 - 720 mV, the ferrocene is oxided, and transfers a
single electron to the electrode via the conductive oligomer. However, the ETM is unable to accept

25 any electrons from the luminol electron source, since the voltages are less than the redox potential of
the luminol. However, at or above the redox potential of luminol, the luminol then transfers an
electron to the ETM, allowing rapid and repeated electron transfer. In this way, the electron source (or
co-reductant) serves to amplify the signal generated in the system, as the electron source molecules
rapidly and repeatedly donate electrons to the ETM of the label probe.

30

Luminol has the added benefit of becoming a chemiluminiscent species upon oxidation (see Jirka et
al., Analytica Chimica Acta 284:345 (1993)), thus allowing photo-detection of electron transfer from the
ETM to the electrode. Thus, as long as the luminol is unable to contact the electrode directly, i.e. in
the presence of the SAM such that there is no efficient electron transfer pathway to the electrode,
35 luminol can only be oxidized by transferring an electron to the ETM on the label probe. When the ETM
is not present, i.e. when the target sequence is not hybridized to the composition of the invention,
luminol is not significantly oxidized, resulting in a low photon emission and thus a low (if any) signal

-81 -

from the luminol. In the presence of the target, a much larger signal is generated. Thus, the measure
of luminol oxidation by photon emission is an indirect measurement of the ability of the ETM to donate
electrons to the electrode. Furthermore, since photon detection is generally more sensitive than
electronic detection, the sensitivity of the system may be increased. Initial results suggest that
5 luminescence may depend on hydrogen peroxide concentration, pH, and luminol concentration, the
latter of which appears to be non-linear.

Suitable electron source molecules are well known in the art, and include, but are not limited to,
ferricyanide, and luminol.

10

Alternatively, output electron acceptors or sinks could be used, i.e. the above reactions could be run in
reverse, with the ETM such as a metallocene receiving an electron from the electrode, converting it to
the metallicenium, with the output electron acceptor then accepting the electron rapidly and
repeatedly. In this embodiment, cobalticenium is the preferred ETM.

15

The presence of the ETMs at the surface of the monolayer can be detected in a variety of ways. A
variety of detection methods may be used, including, but not limited to, optical detection (as a result of
spectral changes upon changes in redox states), which includes fluorescence, phosphorescence,
luminiscence, chemiluminescence, electrochemiluminescence, and refractive index; and electronic
20 detection, including, but not limited to, amperommetry, voltammetry, capacitance and impedence.

These methods include time or frequency dependent methods based on AC or DC currents, pulsed
methods, lock-in techniques, filtering (high pass, low pass, band pass), and time-resolved techniques
including time-resolved fluoroscence.

25 In one embodiment, the efficient transfer of electrons from the ETM to the electrode results in

stereotyped changes in the redox state of the ETM. With many ETMs including the complexes of
ruthenium containing bipyridine, pyridine and imidazole rings, these changes in redox state are
associated with changes in spectral properties. Significant differences in absorbance are observed
between reduced and oxidized states for these molecules. See for example Fabbrizzi et al., Chem.

30 Soc. Rev. 1995 pp1 97-202). These differences can be monitored using a spectrophotometer or
simple photomultiplier tube device.

In this embodiment, possible electron donors and acceptors include all the derivatives listed above for
photoactivation or initiation. Preferred electron donors and acceptors have characteristically large
35 spectral changes upon oxidation and reduction resulting in highly sensitive monitoring of electron
transfer. Such examples include Ru(NH 3 ) 4 py and Ru(bpy) 2 im as preferred examples. It should be

-82 -

understood that only the donor or acceptor that is being monitored by absorbance need have ideal
spectral characteristics.

In a preferred embodiment, the electron transfer is detected fluorometrically. Numerous transition
5 metal complexes, including those of ruthenium, have distinct fluorescence properties. Therefore, the
change in redox state of the electron donors and electron acceptors attached to the nucleic acid can
be monitored very sensitively using fluorescence, for example with Ru(4,7-biphenyl 2 -phenanthroline) 3 2 ' i '
. The production of this compound can be easily measured using standard fluorescence assay
techniques. For example, laser induced fluorescence can be recorded in a standard single cell
10 fluorimeter, a flow through "on-line" fluorimeter (such as those attached to a chromatography system)
or a multi-sample "plate-reader" similar to those marketed for 96-well immuno assays.

Alternatively, fluorescence can be measured using fiber optic sensors with nucleic acid probes in
solution or attached to the fiber optic. Fluorescence is monitored using a photomultiplier tube or other
15 light detection instrument attached to the fiber optic. The advantage of this system is the extremely
small volumes of sample that can be assayed.

In addition, scanning fluorescence detectors such as the Fiuorlmager sold by Molecular Dynamics are
ideally suited to monitoring the fluorescence of modified nucleic acid molecules arrayed on solid
20 surfaces. The advantage of this system is the large number of electron transfer probes that can be
scanned at once using chips covered with thousands of distinct nucleic acid probes.

Many transition metal complexes display fluorescence with large Stokes shifts. Suitable examples
include bis- and trisphenanthroline complexes and bis- and trisbipyridyl complexes of transition metals

25 such as ruthenium (see Juris, A., Balzani, V., et. al. Coord. Chem. Rev., V. 84, p. 85-277, 1988).

Preferred examples display efficient fluorescence (reasonably high quantum yields) as well as low
reorganization energies. These include Ru(4,7-biphenyl 2 -phenanthroline) 3 2+ , Ru(4,4'-diphenyl-2,2'-
bipyridine) 3 2+ and platinum complexes (see Cummings et al., J. Am. Chem. Soc. 118:1949-1960
(1996), incorporated by reference). Alternatively, a reduction in fluorescence associated with

30 hybridization can be measured using these systems.

In a further embodiment, electrochemiluminescence is used as the basis of the electron transfer
detection. With some ETMs such as Ru 2+ (bpy) 3 , direct luminescence accompanies excited state
decay. Changes in this property are associated with nucleic acid hybridization and can be monitored
35 with a simple photomultiplier tube arrangement (see Blackburn, G. F. Clin. Chem. 37: 1534-1539
(1991); and Juris etal., supra.

-83-

In a preferred embodiment, electronic detection is used, including amperommetry, voltammetry,
capacitance, and impedence. Suitable techniques include, but are not limited to, electrogravimetry;
coulometry (including controlled potential coulometry and constant current coulometry); voltametry
(cyclic voltametry, pulse voltametry (normal pulse voltametry, square wave voltametry, differential
5 pulse voltametry, Osteryoung square wave voltametry, and coulostatic pulse techniques); stripping
analysis (aniodic stripping analysis, cathiodic stripping analysis, square wave stripping voltammetry);
conductance measurements (electrolytic conductance, direct analysis); time-dependent
electrochemical analyses (chronoamperometry, chronopotentiometry, cyclic chronopotentiometry and
amperometry, AC polography, chronogalvametry, and chronocoulometry); AC impedance
10 measurement; capacitance measurement; AC voltametry; and photoelectrochemistry.

In a preferred embodiment, monitoring electron transfer is via amperometric detection. This method of
detection involves applying a potential (as compared to a separate reference electrode) between the
nucleic acid-conjugated electrode and a reference (counter) electrode in the sample containing target
15 genes of interest. Electron transfer of differing efficiencies is induced in samples in the presence or

absence of target nucleic acid; that is, the presence or absence of the target nucleic acid, and thus the
label probe, can result in different currents.

The device for measuring electron transfer amperometrically involves sensitive current detection and
20 includes a means of controlling the voltage potential, usually a potentiostat. This voltage is optimized
with reference to the potential of the electron donating complex on the label probe. Possible electron
donating complexes include those previously mentioned with complexes of iron, osmium, platinum,
cobalt, rhenium and ruthenium being preferred and complexes of iron being most preferred.

25 In a preferred embodiment, alternative electron detection modes are utilized. For example,

potentiometric (or voltammetric) measurements involve non-faradaic (no net current flow) processes
and are utilized traditionally in pH and other ion detectors. Similar sensors are used to monitor
electron transfer between the ETM and the electrode. In addition, other properties of insulators (such
as resistance) and of conductors (such as conductivity, impedance and capicitance) could be used to

30 monitor electron transfer between ETM and the electrode. Finally, any system that generates a

current (such as electron transfer) also generates a small magnetic field, which may be monitored in
some embodiments.

It should be understood that one benefit of the fast rates of electron transfer observed in the
35 compositions of the invention is that time resolution can greatly enhance the signal-to-noise results of
monitors based on absorbance, fluorescence and electronic current. The fast rates of electron
transfer of the present invention result both in high signals and stereotyped delays between electron

-84-

transfer initiation and completion. By amplifying signals of particular delays, such as through the use
of pulsed initiation of electron transfer and "lock-in" amplifiers of detection, and Fourier transforms.

In a preferred embodiment, electron transfer is initiated using alternating current (AC) methods.
5 Without being bound by theory, it appears that ETMs, bound to an electrode, generally respond

similarly to an AC voltage across a circuit containing resistors and capacitors. Basically, any methods
which enable the determination of the nature of these complexes, which act as a resistor and
capacitor, can be used as the basis of detection. Surprisingly, traditional electrochemical theory, such
as exemplified in Laviron etal., J. Electroanal. Chem. 97:135 (1979) and Laviron etal., J. Electroanal.
10 Chem. 105:35 (1979), both of which are incorporated by reference, do not accurately model the

systems described herein, except for very small E AC (less than 10 mV) and relatively large numbers of
molecules. That is, the AC current (I) is not accurately described by Laviron's equation. This may be
due in part to the fact that this theory assumes an unlimited source and sink of electrons, which is not
true in the present systems.

15

The AC voltametry theory that models these systems well is outlined in O'Connor et al., J. Electroanal.
Chem. 466(2): 197-202 (1999), hereby expressly incorporated by reference. The equation that
predicts these systems is shown below as Equation 1:

Equation 1

smh[— -E AC ]

cosh[— -E^ c ] +cosh[— (E DC -E 0 )]

20 In Equation 1 , n is the number of electrons oxidized or reduced per redox molecule, f is the applied
frequency, F is Faraday's constant, N total is the total number of redox molecules, E 0 is the formal
potential of the redox molecule, R is the gas constant, T is the temperature in degrees Kelvin, and E DC
is the electrode potential. The model fits the experimental data very well. In some cases the current is
smaller than predicted, however this has been shown to be caused by ferrocene degradation which

25 may be remedied in a number of ways.

In addition, the faradaic current can also be expressed as a function of time, as shown in Equation 2:

Equation 2

% N tot a i nF dV(t)

I r [t) - nF dt

2RT{cosh[ (V( t) -E ) ] +1)

v RT o J

-85 -

I F is the Faradaic current and q e is the elementary charge.

However, Equation 1 does not incorporate the effect of electron transfer rate nor of instrument factors.
Electron transfer rate is important when the rate is close to or lower than the applied frequency. Thus,
5 the true i AC should be a function of all three, as depicted in Equation 3.

Equation 3

Uc = f(Nernst factors)f(k ET )f(instrument factors)

These equations can be used to model and predict the expected AC currents in systems which use
10 input signals comprising both AC and DC components. As outlined above, traditional theory
surprisingly does not model these systems at all, except for very low voltages.

In general, non-specifically bound label probes/ETMs show differences in impedance (i.e. higher
impedances) than when the label probes containing the ETMs are specifically bound in the correct
15 orientation. In a preferred embodiment, the non-specifically bound material is washed away, resulting
in an effective impedance of infinity. Thus, AC detection gives several advantages as is generally
discussed below, including an increase in sensitivity, and the ability to "filter out" background noise. In
particular, changes in impedance {including, for example, bulk impedance) as between non-specific
binding of ETM-containing probes and target-specific assay complex formation may be monitored.

20

Accordingly, when using AC initiation and detection methods, the frequency response of the system
changes as a result of the presence of the ETM. By "frequency response" herein is meant a
modification of signals as a result of electron transfer between the electrode and the ETM. This
modification is different depending on signal frequency. A frequency response includes AC currents at
25 one or more frequencies, phase shifts, DC offset voltages,, faradaic impedance, etc.

Once the assay complex including the target sequence and label probe is made, a first input electrical
signal is then applied to the system, preferably via at least the sample electrode (containing the
complexes of the invention) and the counter electrode, to initiate electron transfer between the

30 electrode and the ETM. Three electrode systems may also be used, with the voltage applied to the

reference and working electrodes. The first input signal comprises at least an AC component. The AC
component may be of variable amplitude and frequency. Generally, for use in the present methods,
the AC amplitude ranges from about 1 mV to about 1.1V, with from about 1 0 mV to about 800 mV
being preferred, and from about 10 mV to about 500 mV being especially preferred. The AC

35 frequency ranges from about 0.01 Hz to about 100 MHz, with from about 10 Hz to about 10 MHz being
preferred, and from about 100 Hz to about 20 MHz being especially preferred.

-86-

The use of combinations of AC and DC signals gives a variety of advantages, including surprising
sensitivity and signal maximization.

In a preferred embodiment, the first input signal comprises a DC component and an AC component.

5 That is, a DC offset voltage between the sample and counter electrodes is swept through the

electrochemical potential of the ETM (for example, when ferrocene is used, the sweep is generally
from 0 to 500 mV) (or alternatively, the working electrode is grounded and the reference electrode is
swept from 0 to -500 mV). The sweep is used to identify the DC voltage at which the maximum
response of the system is seen. This is generally at or about the electrochemical potential of the ETM.

1 0 Once this voltage is determined, either a sweep or one or more uniform DC offset voltages may be

used. DC offset voltages of from about -1 V to about +1 .1 V are preferred, with from about -500 mV to
about +800 mV being especially preferred, and from about -300 mV to about 500 mV being particularly
preferred. In a preferred embodiment, the DC offset voltage is not zero. On top of the DC offset
voltage, an AC signal component of variable amplitude and frequency is applied. If the ETM is

15 present, and can respond to the AC perturbation, an AC current will be produced due to electron
transfer between the electrode and the ETM.

For defined systems, it may be sufficient to apply a single input signal to differentiate between the
presence and absence of the ETM (i.e. the presence of the target sequence) nucleic acid.
20 Alternatively, a plurality of input signals are applied. As outlined herein, this may take a variety of

forms, including using multiple frequencies, multiple DC offset voltages, or multiple AC amplitudes, or
combinations of any or all of these.

Thus, in a preferred embodiment, multiple DC offset voltages are used, although as outlined above,
25 DC voltage sweeps are preferred. This may be done at a single frequency, or at two or more
frequencies .

In a preferred embodiment, the AC amplitude is varied. Without being bound by theory, it appears that
increasing the amplitude increases the driving force. Thus, higher amplitudes, which result in higher

30 overpotentials give faster rates of electron transfer. Thus, generally, the same system gives an
improved response (i.e. higher output signals) at any single frequency through the use of higher
overpotentials at that frequency. Thus, the amplitude may be increased at high frequencies to
increase the rate of electron transfer through the system, resulting in greater sensitivity. In addition,
this may be used, for example, to induce responses in slower systems such as those that do not

35 possess optimal spacing configurations.

- 87 -

*

In a preferred embodiment, measurements of the system are taken at at least two separate amplitudes
or overpotentials, with measurements at a plurality of amplitudes being preferred. As noted above,
changes in response as a result of changes in amplitude may form the basis of identification,
calibration and quantification of the system. In addition, one or more AC frequencies can be used as
5 well.

In a preferred embodiment, the AC frequency is varied. At different frequencies, different molecules
respond in different ways. As will be appreciated by those in the art, increasing the frequency
generally increases the output current. However, when the frequency is greater than the rate at which
10 electrons may travel between the electrode and the ETM, higher frequencies result in a loss or
decrease of output signal. At some point, the frequency will be greater than the rate of electron
transfer between the ETM and the electrode, and then the output signal will also drop.

In one embodiment, detection utilizes a single measurement of output signal at a single frequency.

1 5 That is, the frequency response of the system in the absence of target sequence, and thus the

absence of label probe containing ETMs, can be previously determined to be very low at a particular
high frequency. Using this information, any response at a particular frequency, will show the presence
of the assay complex. That is, any response at a particular frequency is characteristic of the assay
complex. Thus, it may only be necessary to use a single input high frequency, and any changes in

20 frequency response is an indication that the ETM is present, and thus that the target sequence is
present.

In addition, the use of AC techniques allows the significant reduction of background signals at any
single frequency due to entities other than the ETMs, i.e. "locking out" or "filtering" unwanted signals.

25 That is, the frequency response of a charge carrier or redox active molecule in solution will be limited
by its diffusion coefficient and charge transfer coefficient. Accordingly, at high frequencies, a charge
carrier may not diffuse rapidly enough to transfer its charge to the electrode, and/or the charge
transfer kinetics may not be fast enough. This is particularly significant in embodiments that do not
have good monolayers, i.e. have partial or insufficient monolayers, i.e. where the solvent is accessible

30 to the electrode. As outlined above, in DC techniques, the presence of "holes" where the electrode is
accessible to the solvent can result in solvent charge carriers "short circuiting" the system, i.e. the
reach the electrode and generate background signal. However, using the present AC techniques, one
or more frequencies can be chosen that prevent a frequency response of one or more charge carriers
in solution, whether or not a monolayer is present. This is particularly significant since many biological

35 fluids such as blood contain significant amounts of redox active molecules which can interfere with
amperometric detection methods.

-88-

In a preferred embodiment, measurements of the system are taken at at least two separate
frequencies, with measurements at a plurality of frequencies being preferred. A plurality of
frequencies includes a scan. For example, measuring the output signal, e.g., the AC current, at a low
input frequency such as 1 - 20 Hz, and comparing the response to the output signal at high frequency
5 such as 10 - 100 kHz will show a frequency response difference between the presence and absence
of the ETM. In a preferred embodiment, the frequency response is determined at at least two,
preferably at least about five, and more preferably at least about ten frequencies.

After transmitting the input signal to initiate electron transfer, an output signal is received or detected.

10 The presence and magnitude of the output signal will depend on a number of factors, including the

overpotential/amplitude of the input signal; the frequency of the input AC signal; the composition of the
intervening medium; the DC offset; the environment of the system; the nature of the ETM; the solvent;
and the type and concentration of salt. At a given input signal, the presence and magnitude of the
output signal will depend in general on the presence or absence of the ETM, the placement and

15 distance of the ETM from the surface of the monolayer and the character of the input signal. In some
embodiments, it may be possible to distinguish between non-specific binding of label probes and the
formation of target specific assay complexes containing label probes, on the basis of impedance.

In a preferred embodiment, the output signal comprises an AC current. As outlined above, the
20 magnitude of the output current will depend on a number of parameters. By varying these parameters,
the system may be optimized in a number of ways.

In general, AC currents generated in the present invention range from about 1 femptoamp to about 1
milliamp, with currents from about 50 femptoamps to about 100 microamps being preferred, and from
25 about 1 picoamp to about 1 microamp being especially preferred.

In a preferred embodiment, the output signal is phase shifted in the AC component relative to the input
signal. Without being bound by theory, it appears that the systems of the present invention may be
sufficiently uniform to allow phase-shifting based detection. That is, the complex biomolecules of the
30 invention through which electron transfer occurs react to the AC input in a homogeneous manner,

similar to standard electronic components, such that a phase shift can be determined. This may serve
as the basis of detection between the presence and absence of the ETM, and/or differences between
the presence of target-specific assay complexes comprising label probes and non-specific binding of
the label probes to the system components.

35

The output signal is characteristic of the presence of the ETM; that is, the output signal is
characteristic of the presence of the target-specific assay complex comprising label probes and ETMs.

-89-

In a preferred embodiment, the basis of the detection is a difference in the faradaic impedance of the
system as a result of the formation of the assay complex. Faradaic impedance is the impedance of
the system between the electrode and the ETM. Faradaic impedance is quite different from the bulk
or dielectric impedance, which is the impedance of the bulk solution between the electrodes. Many
5 factors may change the faradaic impedance which may not effect the bulk impedance, and vice versa.
Thus, the assay complexes comprising the nucleic acids in this system have a certain faradaic
impedance, that will depend on the distance between the ETM and the electrode, their electronic
properties, and the composition of the intervening medium, among other things. Of importance in the
methods of the invention is that the faradaic impedance between the ETM and the electrode is
10 signficantly different depending on whether the label probes containing the ETMs are specifically or
non-specifically bound to the electrode.

Accordingly, the present invention further provides apparatus for the detection of nucleic acids using
AC detection methods. The apparatus includes a test chamber which has at least a first measuring or
15 sample electrode, and a second measuring or counter electrode. Three electrode systems are also
useful. The first and second measuring electrodes are in contact with a test sample receiving region,
such that in the presence of a liquid test sample, the two electrodes may be in electrical contact.

In a preferred embodiment, the first measuring electrode comprises a single stranded nucleic acid
20 capture probe covalently attached via an attachment linker, and a monolayer comprising conductive
oligomers, such as are described herein.

The apparatus further comprises an AC voltage source electrically connected to the test chamber; that
is, to the measuring electrodes. Preferably, the AC voltage source is capable of delivering DC offset
25 voltage as well.

In a preferred embodiment, the apparatus further comprises a processor capable of comparing the
input signal and the output signal. The processor is coupled to the electrodes and configured to
receive an output signal, and thus detect the presence of the target nucleic acid.

30

Thus, the compositions of the present invention may be used in a variety of research, clinical, quality
control, or field testing settings.

In a preferred embodiment, the probes are used in genetic diagnosis. For example, probes can be
35 made using the techniques disclosed herein to detect target sequences such as the gene for

nonpolyposis colon cancer, the BRCA1 breast cancer gene, P53, which is a gene associated with a
variety of cancers, the Apo E4 gene that indicates a greater risk of Alzheimer's disease, allowing for

-90-

easy presymptomatic screening of patients, mutations in the cystic fibrosis gene, or any of the others
well known in the art.

In an additional embodiment, viral and bacterial detection is done using the complexes of the
5 invention. In this embodiment, probes are designed to detect target sequences from a variety of

bacteria and viruses. For example, current blood-screening techniques rely on the detection of anti-
H1V antibodies. The methods disclosed herein allow for direct screening of clinical samples to detect
HIV nucleic acid sequences, particularly highly conserved HIV sequences. In addition, this allows
direct monitoring of circulating virus within a patient as an improved method of assessing the efficacy
10 of anti-viral therapies. Similarly, viruses associated with leukemia, HTLV-I and HTLV-II, may be

detected in this way. Bacterial infections such as tuberculosis, clymidia and other sexually transmitted
diseases, may also be detected, for example using ribosomal RNA (rRNA) as the target sequences.

In a preferred embodiment, the nucleic acids of the invention find use as probes for toxic bacteria in
15 the screening of water and food samples. For example, samples may be treated to lyse the bacteria
to release its nucleic acid (particularly rRNA), and then probes designed to recognize bacterial strains,
including, but not limited to, such pathogenic strains as, Salmonella, Campylobacter, Vibrio cholerae,
Leishmania, enterotoxic strains of E. coli, and Legionnaire's disease bacteria. Similarly,
bioremediation strategies may be evaluated using the compositions of the invention.

20

In a further embodiment, the probes are used for forensic "DNA fingerprinting" to match crime-scene
DNA against samples taken from victims and suspects.

In an additional embodiment, the probes in an array are used for sequencing by hybridization.

25

Thus, the present invention provides for extremely specific and sensitive probes, which may, in some
embodiments, detect target sequences without removal of unhybridized probe. This will be useful in
the generation of automated gene probe assays.

30 Alternatively, the compositions of the invention are useful to detect successful gene amplification in
PCR, thus allowing successful PCR reactions to be an indication of the presence or absence of a
target sequence. PCR may be used in this manner in several ways. For example, in one
embodiment, the PCR reaction is done as is known in the art, and then added to a composition of the
invention comprising the target nucleic acid with a ETM, covalently attached to an electrode via a

35 conductive oligomer with subsequent detection of the target sequence. Alternatively, PCR is done
using nucleotides labelled with a ETM, either in the presence of, or with subsequent addition to, an
electrode with a conductive oligomer and a target nucleic acid. Binding of the PCR product containing

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ETMs to the electrode composition will allow detection via electron transfer. Finally, the nucleic acid
attached to the electrode via a conductive polymer may be one PCR primer, with addition of a second
primer labelled with an ETM. Elongation results in double stranded nucleic acid with a ETM
and electrode covalently attached. In this way, the present invention is used for PCR detection of
5 target sequences.

In a preferred embodiment, the arrays are used for mRNA detection. A preferred embodiment utilizes
either capture probes or capture extender probes that hybridize close to the 3' polyadenylation tail of
the mRNAs. This allows the use of one species of target binding probe for detection, i.e. the probe
10 contains a poly-T portion that will bind to the poly-A tail of the mRNA target. Generally, the probe will
contain a second portion, preferably non-poly-T, that will bind to the detection probe (or other probe).
This allows one target-binding probe to be made, and thus decreases the amount of different probe
synthesis that is done.

15 In a preferred embodiment, the use of restriction enzymes and ligation methods allows the creation of
"universal" arrays. In this embodiment, monolayers comprising capture probes that comprise
restriction endonuclease ends, as is generally depicted in Figure 7 of PCT US97/20014 . By utilizing
complementary portions of nucleic acid, while leaving "sticky ends", an array comprising any number
of restriction endonuclease sites is made. Treating a target sample with one or more of these

20 restriction endonucleases allows the targets to bind to the array. This can be done without knowing

the sequence of the target. The target sequences can be ligated, as desired, using standard methods
such as ligases, and the target sequence detected, using either standard labels or the methods of the
invention.

25 The present invention provides methods which can result in sensitive detection of nucleic acids. In a
preferred embodiment, less than about 10 X 10 6 molecules are detected, with less than about 10 X 10 s
being preferred, less than 10 X 10 4 being particularly preferred, less than about 10 X 10 3 being
especially preferred, and less than about 10 X 10 2 being most preferred. As will be appreciated by
those in the art, this assumes a 1:1 correlation between target sequences and reporter molecules; if

30 more than one reporter molecule (i.e. electron transfer moeity) is used for each target sequence, the
sensitivity will go up.

While the limits of detection are currently being evaluated, based on the published electron transfer
rate through DNA, which is roughly 1 X 10 s electrons/sec/duplex for an 8 base pair separation (see
35 Meade et al., Angw. Chem. Eng. Ed., 34:352 (1995)) and high driving forces, AC frequencies of about
100 kHz should be possible. As the preliminary results show, electron transfer through these systems

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is quite efficient, resulting in nearly 100 X 10 3 electrons/sec, resulting in potential femptoamp
sensitivity for very few molecules.

The following examples serve to more fully describe the manner of using the above-described
5 invention, as well as to set forth the best modes contemplated for carrying out various aspects of the
invention. It is understood that these examples in no way serve to limit the true scope of this invention,
but rather are presented for illustrative purposes. All references cited herein are incorporated by
reference.

10 EXAMPLES

Example 1

Preparation and Evaluation of Asymmetric Monolayers

15 Preparation of Asymmetric Monolayers
Synthesis of Symmetrical Disulfide

Symmetrical disulfides may be prepared from neopentyl alcohol or from neopentyl iodide in the
presence of thiol acetic acid. Preferably, the reaction is carried out using neopentyl alcohol in the
presence of PPh3 and DIPAD. The resulting disulfide is recrystallized from hexane, purified on a
20 chromatographic column, and treated with sodium hydroxide to yield a symmetrical disulfide (See
Figure 3A).

Synthesis of CT103

The strategy for the synthesis of a precursor for CPG with an AMFS was based on the chemistry
25 established for exchanging an symmetrical disulfide with acetyl thiol moiety in the presence of a base
as shown in Figure 3C. First, CT100 was obtained from dimethyloxetane and thiolacetic acide. Next,
the symmetrical disulfide CT101 was obtained from CT100 by treating CT100 with NaOH and dioxane.
Treatment of K133 and CT101 in the presence of NaOH and Dioxane yielded the asymmetrical
monolayer forming species CT1 02. Further treatment of CT1 02 with succinic anhydride provided
30 CT103. The CPG-CT103 was synthesized as known in the art.

Synthesis of CT105

The synthesis of CT105 is depicted in Figure 3E and involves the following steps:

35

Synthesis of M41. To a flask was added sodium hydride (6.68 g, 60% in mineral oil) to a solution of
triethylene glycol (83.7 g) in 1 L anhydrous DMF. The reaction mixture was stirred for 45 min at room

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temperature, then cool to 0°C in an ice bath. To the mixture was added 1 1-bromo-1-undecene (26 g)
in 100 mL of DMF dropwise within 30 min at 0 °C and then the mixture was vigorously stirred for 1
hour at 0 °C. After removing the cooling bath, the reaction mixture was vigorously stirred overnight at
room temperature. To the mixture was add 50 mL of water, then the solution was concentrated on a
5 high vacuum rotavapor. To the residue was add 400 mL of ethyl acetate and 600 mL of water and the
organic layer was separated, and the aqueous layer was extracted with 30% ethyl acetate/70%
hexane solution (3x 300 mL). The combined organic layers were washed with water (2x300 ml), dried
over anhydrous sodium sulfate, filtered and concentrated. T he residue was purified with silica gel
chromatography eluted with 10% - 70% ethyl acetate in hexane to provide the desired product.

10

Synthesis of M42. To a Shlenk tube were added M41 (7.6 g), thioacetic acid (2.2 mL), and t-butyl
peroxide (0.48 mL). Then the solution was flushed with argon for 5 min. After the cap was closed, the
tube was heated at 100 °C overnight in an oi! bath. The tube was cooled to room temperature, and the
reaction mixture was diluted with 400 mL of dichloromethane. The organic solution was washed with
15 200 mL of 5% sodium bicarbonate. Then the aqueous layer was extracted with dichloromethane (2 x
300 mL). The combined organic layers, was washed with brine, dried over anhydrous sodium sulfate,
filtered and concentrated. The residue was purified with silica gel chromatography eluted with 30% -
50% ethyl acetate in hexane to provide the desired product.

20 Synthesis of CT101 . To a flask was added 3,3-dimethyloxetane (8.25 g, 96 mmol) and thiol acetic
acid (13.06 g, 172 mmol). The reaction mixture was heated to 65 °C in an oil bath for 40 hours. Then
the non-consumed starting material was removed by distillation under vacuum (20-30 mmHg) at 65
°C. The crude product was dissolved in 60 mL of methanol in a round bottom flask and potassium
carbonate (15.6 g) was added. The reaction mixture was vigorously stirred at room temperature in

25 open air for 24 hours. The reaction mixture was filtered through a bed of Celite and washed with a
mixture of methanol and dichloromethane (2:1 , 3 x 50 mL). Then the filtrate was concentrated. The
residue was purified with silica gel chromatography eluted with 1% -5% methanol in dichloromethane
to provide the desired product. 1 H NMR (300 MHz, CDCI 3 ) d 3.48 (s, 2H, CH 2 0), 2.89 (s, 2H, CH 2 S),
1.01 (s, 6H, 2xCH 3 ).

30

Synthesis of CT105. To a flask containing M42 (0.64 g) and CT101(1.0 g) in THF (10 mL) and
methanol (10 mL) was added NaOH solution (1 .0 mL , 8 M). The mixture was stirred in the air for six
hours. Then the solvents were removed on a rotavapor at 40 °C and residue was dissolved in 150 mL
of dichloromethane. The mixture was extracted with water (2x50 mL) and the organic layer dried over
35 anhydrous sodium sulfate, filtered and concentrated. The residue was purified with silica gel

chromatography eluted with 50% -90% ethyl acetate in hexane to provide the desired product as
colorless viscous oil. 1 H NMR (300 MHz, CDCI 3 ) d 3.80 - 3.62 (m, 12H, 6 x OCH 2 ), 3.47 (m, 4H, 2 x

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CH 2 OH), 2.85 (s, 2H, SCH 2 CMe 2 ), 2.74 (t, J = 7.2 Hz, 2H, SCH 2 ), 1.77 - 1.63 (m, 4H, 2 x CH 2 ), 1.32
(m, 16H), 1.02 (s, 6H, CMe 2 ). Anal, calcd. for (C 22 H 46 O s S 2 +Na) + : 477. Found: 477.

Electrochemical Evaluation of New Insulators

The following oligonucleotides were used to evaluate the new insulators:

1) Capture oligonucleotides:

D1650: 5'-TCA TTG ATG GTC TCT TTT AAC A(N1 52)
D1678: 5-GAC TGA CTC GTA CTA(N152)

2) Direct assay signaling probe:

D1085: 5-TCT ACA G(N6) C(N6) TGT TAA AAG AGA CCA TCA ATG A

3) Sandwich Assay target and signaling probes:

D765: 5-GAC ATC AAG CAG CCA TGC AAA TGT TAA AAG AGA CCA TCA ATG AGG
AAG CTG CAG AAT GGG ATA GAG TGC ATC CAG T

D772: 5'-(N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) G(C131) TTT GCA
TGG CTG CTT GAT GTC

D1 1 56: 5'-CAC AGT GGG GGG ACA TCA AGC AGC CAT GCA AAT GTT AAA AGA GAC
CAT CAA TGA GGA AGC TGC AGA ATG GGA TAG AGT CAT CCA GT
D1355 (20 Fc), D1356 (30 Fc) and D1357 (36 Fc) have the similar sequence as DI358 (54 (Fc):
D 1358: 5'-(C23)(C23)(C23)(C23)(C23)(C23)(N87)(N87)(N87)(N87) ATC (C140)(N87)
(N 87)(N87)(N87)(C140) TTT GCA TGG CTG CTT GAT GTC CCC CCA CTG TG
D998: 5'- TGT GCA GTT GAC GTG GAT TGT TAA AAG AGA CCA TCA ATG AGG AAG
CTG CAG AAT GGG ATA GAG TCA TCC AGT

D1055 (20Fc): 5'-(C23)(C23)(C23)(C23)(N87)(N87)(N87)(N87)(C140) ATC CAC GTC AAC
TGC ACA

Chip preparation and deposition solution .

Chips were made on spotting machine. To diminish the effect of chip materials, the chips with
different insulators were made from the same circuit board. An array chip (lot # DC228, DC229, and
DC231, Type CB37-4) with sensor pads containing self assembled monolayer according to
the pattern shown in Figure 10.

The pad surfaces were respectively treated with the deposition solutions. To reduce the influence of
the concentration of capture oligonucleotides, a stock deposition solution was prepared according
tothe standard procedure without insulator. Next, the stock solution was divided into three portions,
into which the insulators, M44, CT99 and CT105, were added respectively. The final deposition

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solutions consisted of a mixture of DNA/H6-two-unit wire/insulator (with ratio of 1/10/5) with a total thiol
concentration of 53 pM. The pads are deposited using the spotting machine and post treated with
insulator. As shown in Figure 10, the chip has two rows of capture pads (D1650), a row of negative
control pads (D1678) non-specific binding pads (D1678), and a row of insulator. The DNA-probe of
5 D1650 is complementary to the target oligonucleotide D1085, D765, D998, and D1156. D1678 is non-
complementary to either target or signaling oligonucleotides.

Hybridization solution and testing .

For direct assays, the solution consists of 200 nM of signaling probe and 41% H 2 0, 25% 4000 mM
10 NaCI0 4 with 80 mM Tris (pH 6.5) 1 .0 mM C6 insulator, 10% FCS, and 24% lysis buffer.

For sandwich assays, the hybridization solution consisted of 10 nM target oligonucleotides and 30 nM
signaling molecule in the mixture of 41% H 2 0, 25% 4000 nM NaCI0 4 with 80 mM Tris, pH 6.5, 1.0 mM
C6 insulator, 10% FCS, and 24% lysis buffer.

^5

rn The hybridization solution is injected into the cartridge of 3 chips. The solution is allowed to hybridize

at room temperature for 2 hours for direct assays or for overnight for sandwich assays. The chip is
,U then plugged into the reader and scanned in 4th harmonics at different frequencies.

ss 'lo All peaks are calculated using the auto peak finder. Ip of each data set (at least three chips) and the

Q standard deviation at all of the frequencies are calculated. The normalized frequency response is

r „ determined by Ip (high frequency)/lp(10 Hz) x folds increase in frequency).

M As shown in Figure 1 1 (direct assay of 2 N6 ferrocene signaling probe), Figure 12 (sandwich assay of

J;; 8 N6 ferrocene), Figure 13 (sandwich assay of 20 C23 type ferrocene) and Figure 14 (sandwich assay

25 for 54 C23 type ferrocene), the new insulators, CT99 and CT105, gave much better electrochemical
response than control insulator M44. All data were collected for 1000 Hz at 4 th harmonics.

However, the nonspecific binding of three different insulators is similar. Figure 15 and Figure 16,
illustrate nonspecific binding for direct and sandwich assays at 1000 Hz and 4 th harmonics. Non-
30 specific signaling on the pads with insulator alone was higher for the new insulators, CT99 and CT105,
but there were no difference on pads containing non complementary DNA.

Figure 17 depicts a monolayer comprising insulators only (i.e. M44) and a monolayer comprising
asymmetric monolayer forming species (i.e. CT105).

35

In order to further evaluate the behavior of the new insulators, a frequency response study was carried
out at 10 Hz, 100 Hz and 100 Hz. As shown in Figures 18-20, the new insulators gave better

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frequency response than the control insulator M44. Figure 18 is the frequency response for D1085 of
two N6 ferrocenes, while Figure 19 and Figure 20, respectively are the frequency response for the
sandwich assays of 8 and 20 ferrocene systems.

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